Re: 13C relaxation Model-free

[Edward d'Auvergne]

On 3 April 2017 at 16:02, Troels Emtekær Linnet  wrote:
> Hi Sahil.
>
> Try the tutorials listed here:
>
> http://wiki.nmr-relax.com/Category:Tutorials
> http://wiki.nmr-relax.com/Tutorial_for_the_relaxation_dispersion_auto-analysis_in_the_GUI
> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi
> http://wiki.nmr-relax.com/Manual
>
> I can get access to the wiki on my chrome, so it should work.
>
> Note, most of the tutorials has been written to the dataformat of Varian.
> And some of the tutorials has been written to a more "general" dataformat.
>
>
> If you have problems with getting the tutorials to work, I could write a
> new tutorial for you.
>
> That would need:
> * An overview of experiments, which field strength, etc.
> * Some sample files with the format. You can limit the amount of data to
> 1-2 spins, to keep confidentiality.

Hi Sahil,

Have you been able to work out how to use the relax GUI for your data?
 Do you have multiple field strength data?  Is this data for a pure
dipole system, or do you have multipole relaxation present?  Note that
the relax trunk does not handle multipole relaxation at the moment.

Regards,

Edward

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Re: S^2 differences between proteins

[Edward d'Auvergne]

On 3 March 2017 at 19:51, Mahdi, Sam  wrote:
> Hello everyone,
>
> This isn't as much a problem with relax as it is a general question
> regarding S^2 values itself. When comparing different values of S^2 between
> proteins, what difference is considered significant. Due to the lower
> values I know say an average S^2 value of .1 is a big difference in the
> flexibility of one protein to another, but what about say an average
> difference of .01, is that still considered a significant change in
> considering the relative dynamics of one protein to another? (I.e. if say,
> protein A has an average S^2 value of 9, and protein B has an average S^2
> value of 8.9, could you make the statement Protein A has significant
> dynamic differences, more rigid, when compared to Protein B. Or could you
> make the statement due to only a difference of .01, there isn't much of a
> overall dynamic difference between the 2 proteins)?

Hi Sam,

Sorry for not getting back to you earlier, I have been extremely busy
lately!  This is really a statistical problem.  And it depends on the
quality of your parameter error estimates.  If you have two values and
two associated errors, then you can look at hypothesis testing / ANOVA
statistics to tell you if the two values are statistically different
(i.e. 1st year Uni stats).  Note that your error estimates should
include the variability of the diffusion tensor, as that will account
for probably around 80% of the influence on the relaxation data, and
without this variability a S2 parameter comparison is meaningless.
There is no rule for S2 differences so you need to rely on basic
statistical tests.

Regards,

Edward

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Re: Relax app MacOS run script

[Edward d'Auvergne]

On 21 April 2017 at 11:02, Pavel Macek  wrote:
> Hi Edward,
> I have issues running the relax script from terminal on MacOs.
>
> I installed relax using the downoladed dmg instaler relax-4.0.3.Darwin.dmg.
> 
> In principle the relax works, although I face some issues loading the peak
> intensities relaxation dispersion. Here when I select the file it is not
> displayed in the "The file name(s)" field unless I press the "nagnifying
> glass" icon in the read file pop-up window.

Hi Pavel,

For this issue, could you please create a bug report at
https://gna.org/bugs/?func=additem=relax ?  That will hopefully
help me replicate the issue, assuming it is not dependent on the OS X
version, and then fix it.  It however sounds like a bug in wxPython.

Cheers,

Edward

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Re: Relax app MacOS run script

[Edward d'Auvergne]

On 24 April 2017 at 20:28, Troels Emtekær Linnet  wrote:
> Dear Pavel.
>
> Welcome to the relax mailing list.
>
> For the .dmg installation, it is only possible to use the GUI.
>
> But you can install relax another way.
>
> Have a look here.
> http://wiki.nmr-relax.com/Category:Installation

Hi,

Let me add that after launching the relax GUI from the Mac App, you
can run scripts directly from the 'User functions->script' menu.  Mac
Apps are designed to be GUI only ;)  If you want to be a power user
and use the command line directly, then you need to follow Troels'
advice.  Troels has created awesomely detailed resources on the relax
wiki for this.

Regards,

Edward

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Re: Error in model free analysis

[Edward d'Auvergne]

Hi Ashish,

I had a look at the results file, and I think the problem is that you
are loading a corrupted PDB file format.  The Z coordinates for all
atoms is set to None!  You can see this at the bottom of the file.
The first few coordinates are:


[-14.56, -14.35, -12.87, -12.01, -14.73, -16.17, ...
[snip]


[6.0, 2.0, 9.0, 1.0, 5.0, 7.0, ...
[snip]


[None, None, None, None, None, None, ...


Because of the strange coordinates, especially integers for the Y
coordinate and nothing for the Z, this can only be an incorrectly
formatted PDB file.  Note that the character position is what counts
in the PDB format.  Could this be the reason?

Regards,

Edward



On 22 February 2017 at 12:01, Ashish Sethi  wrote:
> Hi Troels,
>
>
>
> I am having troubles login to my account. So I have uploaded the results.bz2 
> file on my drop box and this is the link to it:
>
>
> https://www.dropbox.com/s/86teapt1isbo8zr/results.bz2?dl=0
>
>
>
> Hope this helps to access the files.
>
>
> Thanks
>
>
> Ashish
>
> 
> From: tlin...@gmail.com  on behalf of Troels Emtekær 
> Linnet 
> Sent: Wednesday, February 22, 2017 8:02:24 PM
> To: Ashish Sethi
> Cc: relax-users@gna.org
> Subject: Re: Error in model free analysis
>
> Hi Ashish.
>
> Attachments to the mailserver is dropped.
> Can you provide a bug report instead, at upload the file there?
>
> https://gna.org/bugs/?func=additem=relax
>
> Best
> Troels
>
> 2017-02-22 8:56 GMT+01:00 Ashish Sethi 
> >:
> Dear Edward,
>
>
>
> I also tried running the same calculation on my personal macbook pro (OSx EI 
> Capitan) and I got the following errors:
>
>
> relax> results.read(file='results', dir='/Users/ashishsethi/Desktop/model 
> free LDLamodule/local_tm/aic')
>
> Opening the file '/Users/ashishsethi/Desktop/model free 
> LDLamodule/local_tm/aic/results.bz2' for reading.
>
> Exception raised in thread.
>
>
> Traceback (most recent call last):
>
>   File "gui/analyses/execute.pyc", line 87, in run
>
>   File "gui/analyses/auto_model_free.pyc", line 811, in run_analysis
>
>   File "auto_analyses/dauvergne_protocol.pyc", line 246, in __init__
>
>   File "auto_analyses/dauvergne_protocol.pyc", line 652, in execute
>
>   File "prompt/uf_objects.pyc", line 225, in __call__
>
>   File "pipe_control/results.pyc", line 97, in read
>
>   File "data_store/__init__.pyc", line 512, in from_xml
>
>   File "data_store/pipe_container.pyc", line 244, in from_xml
>
>   File "lib/structure/internal/object.pyc", line 1714, in from_xml
>
>   File "lib/structure/internal/models.pyc", line 155, in from_xml
>
>   File "lib/structure/internal/molecules.pyc", line 632, in from_xml
>
>   File "lib/structure/internal/molecules.pyc", line 449, in from_xml
>
>   File "lib/xml.pyc", line 287, in xml_to_object
>
>   File "lib/float.pyc", line 200, in packBytesAsPyFloat
>
> error: pack expected 8 items for packing (got 571)
>
>
>
> I have attached the results.bz2 file with this email.
>
>
>
> Thanks
>
>
> Ashish
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Re: Error in setting up model free analysis

[Edward d'Auvergne]

On 21 February 2017 at 07:29, Ashish Sethi  wrote:
> Thanks Sam.
>
>
>
> I did ignore the error message and run the model free analysis and I got the 
> following errors:
>
>
>
> Traceback (most recent call last):
>   File "/usr/local/relax/gui/analyses/execute.py", line 87, in run
> self.run_analysis()
>   File "/usr/local/relax/gui/analyses/auto_model_free.py", line 808, in 
> run_analysis
> dauvergne_protocol.dAuvergne_protocol(pipe_name=self.data.pipe_name, 
> pipe_bundle=self.data.pipe_bundle, results_dir=self.data.save_dir, 
> diff_model=self.data.global_models, mf_models=self.data.mf_models, 
> local_tm_models=self.data.local_tm_models, grid_inc=self.data.inc, 
> diff_tensor_grid_inc=self.data.diff_tensor_grid_inc, 
> mc_sim_num=self.data.mc_sim_num, max_iter=self.data.max_iter, 
> conv_loop=self.data.conv_loop)
>   File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 241, in 
> __init__
> self.execute()
>   File "/usr/local/relax/auto_analyses/dauvergne_protocol.py", line 604, in 
> execute
> self.interpreter.results.read(file='results', 
> dir=self.results_dir+'local_tm'+sep+'aic')
>   File "/usr/local/relax/prompt/uf_objects.py", line 221, in __call__
> self._backend(*new_args, **uf_kargs)
>   File "/usr/local/relax/generic_fns/results.py", line 96, in read
> ds.from_xml(file, dir=dirname(file_path), pipe_to=pipes.cdp_name())
>   File "/usr/local/relax/data/__init__.py", line 452, in from_xml
> self[pipe_to].from_xml(pipe_nodes[0], dir=dir, file_version=file_version)
>   File "/usr/local/relax/data/pipe_container.py", line 255, in from_xml
> self.structure.from_xml(str_nodes[0], dir=dir, id=parser, 
> file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 296, in 
> from_xml
> self.structural_data.from_xml(model_nodes, id=id, 
> file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 1223, in 
> from_xml
> self[-1].mol.from_xml(mol_nodes, id=id, file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/api_base.py", line 1441, in 
> from_xml
> self[-1].from_xml(mol_node, file_version=file_version)
>   File "/usr/local/relax/generic_fns/structure/internal.py", line 2607, in 
> from_xml
> xml_to_object(mol_node, self, file_version=file_version)
>   File "/usr/local/relax/data/relax_xml.py", line 277, in xml_to_object
> value[i] = packBytesAsPyFloat(ieee_value[i])
>   File "/usr/local/relax/float.py", line 200, in packBytesAsPyFloat
> doubleString=pack('8B',*bytes)
> error: pack expected 8 items for packing (got 571)
>
>
>
> Can anyone suggest what is the problem ?

Hi Ashish,

Such an error message means that the relax results file is corrupted
somehow.  Maybe check that you haven't run out of hard disk space or
that there are no bad sectors on the hard disk.  You could also open
up the results_dir+local_tm/aic/results.bz2 file and see if that file
looks ok.  If there is nothing wrong with your hard disk, could you
open up a bug report at https://gna.org/bugs/?func=additem=relax
and attach the results.bz2 file causing the problem?  If you'd like to
keep your data private, try deleting residues from the XML file until
you only have 1 or 2 left, and use the state.load user function to
make sure that that exact "error: pack expected 8 items for packing
(got 571)" message is still present.

Regards,

Edward

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Re: Error in setting up model free analysis

[Edward d'Auvergne]

On 21 February 2017 at 05:40, Ashish Sethi  wrote:
> Dear Edward,
>
>
> Hope this email finds you well !!!
>
>
>
> I am a beginner in the field of protein dynamics and I wish to do a model 
> free analysis for my protein which is about 72 residues (8.5 kDa). I have 
> calculated the standard R1, R2 and NOE (steady state) parameters and also did 
> the reduced spectral density mapping.
>
>
> My question is related to dipolar relaxation settings while setting up the 
> model free analysis, so all my files (R1, R2 and NOE) only have 15N spin 
> information and if I follow the instructions given in the manual and select 
> "@N" and "@H"-- i get an error saying no information available for H spin 
> which is obvious. In this case what am I supposed to select ? Apologies for 
> my naivety.

Hi Ashish,

Welcome to the relax mailing lists!  Note for a model-free analysis
that for over 2 decades now it is expected that you collect data at 2
or more field strengths.  I suggest you have a read of the following
reference to understand why a model-free analysis fails - i.e. you end
up with artificial Rex and nanosecond motions:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494.  (http://dx.doi.org/10.1039/b702202f).

As for the error, this should actually be a RelaxWarning saying that
the H spins are deselected as there is no relaxation data.  If you
have a RelaxError, or any other Python Error, could you copy and paste
that error message?  Otherwise, the RelaxWarning is what you should
expect.

Regards,

Edward

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Re: Dispersion Back Calculation

[Edward d'Auvergne]

On 15 November 2016 at 14:33, Jeremy Anderson  wrote:
> Hi Edward,
>
> Thanks for the follow up.  I totally understand the reasons for not having
> fixed values within a relax analysis, it seems like a special case relative
> to what I've seen in the literature and increases ones ability to skew the
> results to their liking, I'm doing my best to safeguard against that myself.

No problems.  You do have to be quite careful, as it is far too easy
to fall into an alternative reality that can nicely explain some of
the biology.  Mapping the optimisation space is an essential tool when
constraining certain parameters to see if you are at a well defined
minimum.  For example it can show you if you've just chopped across a
valley in the space and the optimiser is landing at the bottom of that
valley where it has been cut.  If you have access to the ancient, yet
very powerful OpenDX software, you can use the dx.map and dx.execute
relax user functions for this.


> I was able to implement such an analysis in python using the RD models from
> relax as well as the scipy and lmfit packages to both hold the dw parameters
> constant while performing the usual grid search then nonlinear least squares
> minimization and perform a cluster analysis holding the rate constant and/or
> the major population constant amongst all residues.  The code is a bit of a
> mess at the moment but I'm hoping to clean it up and make a repository on
> github, so I can better document what I did and so other folks can check it
> out if they want.

Note that I originally looked at the scipy optimisation packages for
relax.  However I found fatal bugs in all three of the algorithms
implemented at the time (Levenberg-Marquardt being one of them).  The
algorithms appeared to minimise the results, but they were nothing
like what Art Palmer's Modelfree4 found.  I was comparing relax to
Modelfree4 for debugging at the time when implementing the model-free
analysis component.  I don't know if anything has changed since then,
but you really need to be wary and double check whenever you use any
part of scipy.  Anyway, because scipy's optimisation was so terrible,
I decided to write the minfx optimisation library
(https://gna.org/projects/minfx/).  You'll see a record of all of this
in my publication history ;)


> Thanks for your assistance.

You're welcome!

Regards,

Edward

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Re: Dispersion Back Calculation

[Edward d'Auvergne]

On 27 October 2016 at 18:10, Jeremy Anderson  wrote:
> Hi Edward and Troels,
>
> Thanks for pointing me in the right direction.  I had dug around a bit in
> the test_suite directory but wanted to make sure I was looking in the right
> place before I descended into the rabbit hole.
>
> I got the back calculation to work using the
> ./test_suite/shared_data/dispersion/ns_mmq_3site_linear/relax_results/solution.py
> script pretty much as-is, just changing the spin parameters to my liking,
> calculating the curve, and outputting the values (ignoring the data and
> residuals in the output file).
>
> Something I didn't mention is that the reason I've been importing the models
> into ipython is so I can hold parameters constant through my own grid search
> and minimization functions, which I had found somewhere in the documentation
> was not possible inside relax for the minimization.  I originally thought
> this would be easier outside of relax.
>
> The reason for this is because I'm in a situation where I can observe HSQC
> peaks in slow exchange in one variant and skewed populations of one or the
> other peaks in two other variants.  I've been working on using the
> complementary information, in this case the observed dw and the kex from ZZ
> exchange experiments, to investigate multi-state exchange in all variants.
>
> The chem. shift differences of the two skewed variants match the measured
> nicely but the rates from CPMG are ~20 fold higher.  Therefore I wanted to
> check and see if a 3-state model with some parameters held constant would
> have infinite solutions (my assumption) or pop out something interesting and
> be able to distinguish between a couple models of the conformational process
> that I have in mind, which seems like a long shot.
>
> Sorry if thats too much information/way too open-ended but I figured I would
> give some context to the greater situation I have found myself in.  Thanks
> again!

Hi Jeremy,

It is true that you cannot fix a parameter in relax and optimise the
others.  The reason is two-fold.  Firstly the minfx library (
https://gna.org/projects/minfx/ ) does support this functionality.
Secondly, this functionality would be highly abused and a lot of
rubbish results will appear in the scientific literature, with a
detrimental effect on the reputation of the whole NMR field.

Also, I didn't think it was worth the time investment compared to
expanding relax to handle multiple data types at the same time, and
then optimising one set of parameters for all experimental data
simultaneously.  In your case, that would be loading the ZZ exchange
and CPMG data at the same time, and optimising the single model.  This
would be interesting, as the two experiment types contain both
complementary and overlapping information content.  So saying that the
overlapping content should only come from the ZZ experiment might
over-constrain the CPMG experiment due to any biases or experimental
noise from that experiment.  Are you able to set up the problem in
this alternative way in iPython?

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 29 October 2016 at 23:44, Mahdi, Sam  wrote:
> Hi Edward,
>
> I was reading the theory on model free within the manual and I had a quick
> question. The d'Auvergne protocol, is that the model-free analysis in
> reverse with the universal solution?

Yes, that is the technique.

> Or is that the model-free models with
> only the AIC model selection (no universal solution). Both methods were
> under the new-protocol section, so I was confused a bit as to which one the
> d'Auvergne protocol is running.

This is a fragment of the protocol.  It is one part of the iterative
procedure shared with the methods that require an initial, external
diffusion tensor estimate.  The key references to understand all of
this are:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f)

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133.
(http://dx.doi.org/10.1007/s10858-007-9213-3)

Regards,

Edward

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Re: Using modified all models free

[Edward d'Auvergne]

On 1 November 2016 at 22:12, Mahdi, Sam  wrote:
> Hello everyone,
>
> I had a quick question regarding running the single model free run (m4).
> For some proteins we only have data at only one field strength, so I know I
> can't use the d'Auvergene protocol (needs a minimum of 4), so I was
> thinking I could run the all models free model. The problem is, I know
> models m6-m9 are models for another field strength, but since I don't have
> data at another field strength, could I just remove them? Or will relax
> just not run m6-9 since I've only loaded one field strength?

Hi Sam,

The protocol I designed for iteratively optimising and fine tuning the
coupled diffusion tensor + model-free optimisation and model selection
problem will only work with 2 or more fields.  If you would like to
understand this problem, please read:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f)

From this, hopefully you will understand why the NMR field will not
take any results from a single field strength analysis seriously.
Note that this has been the case since the mid 1990's.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 4 October 2016 at 23:23, Mahdi, Sam  wrote:
> Hi Edward,
>
> Just wanted to update you on the status of my runs. I had 2 potential dimer
> structures. I ran Chain A and B for one of them, and Chain B for the other.
> All the results were all very similar. There was missing data though
> throughout (i.e. I had data for some residues for Chain A that had no data
> in Chain B, Or chain A for one pdb file and Chain B for the other pdb file
> would have data, but Chain B for the other pdb file wouldn't). The data that
> is there for all 3 though does make sense. Thank you so much for your help

You're welcome!  Thanks too to Troels and Gary for answering most of
your questions.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 10 October 2016 at 23:12, Mahdi, Sam  wrote:
> Hi Edward,
>
> Wanted to update you a prior problem I had. So I ran relax with multiple
> processors and single processor with the same data set, and obtained
> identical data on my computer. So the previous issue I had with missing data
> I don't think is related to relax itself. Just wanted to let you know.

This is great to hear.  The relax test suite is a gold standard which
shows that this should always be the case.  Though there are a few
extremely minor differences when using different operating systems and
32 vs. 64-bit systems, the code paths for running on the multi and
uni-processors is identical.  This is thanks to Gary Thompson's great
design of the multi-processor system :)

Regards,

Edward

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Re: Dispersion Back Calculation

[Edward d'Auvergne]

On 21 October 2016 at 00:14, Jeremy Anderson  wrote:
> Hello,
>
> I've been trying to back calculate data from parameters using the NS MMQ
> 3-site linear model.  I've tried to do something akin to the
> sample_scripts/model_free/generate_ri.py sample script as described in the
> mail-archive .
> I'm afraid that I'm not knowledgable enough about the data structures,
> parameters, and functions of relax.
>
> Up to this point I have been simulating data using the CR72 and TSMFK01
> dispersion models by importing the R2eff functionality of each module into
> an ipython notebook and supplying parameters interactively.  I've attempted
> this with the NS MMQ 3-site linear model however I'm getting lost in the
> structures of the input parameters.
>
> Ideally what I would like to be able to do is input the parameters:
>
>
> pA, pB, pC = .8, .15, .05
>
> R20A, R20B, R20C = 10, 15, 20 (s^-1)
>
> dw_AB, dw_BC = 2, 2 (ppm)
>
> kex_AB, kex_BC, kex_AC = 400, 200, 0 (s^-1)
>
> dwH_AB, dwH_BC = .2, .2 (ppm)
>
>
> into the r2eff_ns_mmq_3site_mq and/or r2eff_ns_mmq_3site_sq_dq_zq functions
> of the ns_mmq_3site module and populate a back_calc array with R2eff
> values for nu_cpmg = np.logspace(1, 3, 20).  I've done the same with the
> 2-site models I mentioned above but I feel I'm a bit over my head here.
>
> Any help would be greatly appreciated and thanks in advance *and* bravo for
> all the work on relax, its great!

Hi Jeremy,

Welcome to the relax mailing lists!  I was wondering if you were able
to work out what to do from Troels' comment?  He has written a lot of
such data back-calculation scripts which can be found in the
test_suite directories, and if you look for scripts and data in there,
you should hopefully be able to see what to do.  As for all the work,
this is a community project with many contributors:

http://gna.org/project/memberlist.php?group=relax

For example Troels has put a lot of work into the relaxation
dispersion analysis, adding many models and making this part super
fast:

http://wiki.nmr-relax.com/Relax_release_descriptions#relax_3.3.0

Hopefully you'll be able to use relax for your purposes and, if not,
maybe you'll be able to expand relax and contribute a little yourself
;)

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 5 October 2016 at 22:01, Mahdi, Sam  wrote:
> Hi Troels,
>
> The mpirun --np 2 gave no output, so I had to abort the command, but here is
> the output.
> crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__"
> 1.3.1
> crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print
> MPI.COMM_WORLD.Get_rank()"
> ^Ccrowlab: [~]>

Hi Sam,

This result I'm pretty sure shows that mpi4py is not functioning
correctly - i.e. there is an installation problem.  This is what you
should see:

[edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import MPI;
print MPI.COMM_WORLD.Get_rank()"
0
1
[edward@localhost ~]$

Note the printout of 0 and 1.  Maybe try the following:

[edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from
mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.'
%(mpi4py.__version__,
MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
MPI.Get_processor_name()))"
Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain.
[edward@localhost ~]$

If you don't see a printout here, then clearly mpi4py and OpenMPI are
not working together correctly.  Without a printout, your mpi4py is
FUBAR.  Are you using the default OpenMPI and mpi4py packages form
fedora, and you don't have any backports or other non-standard sources
set up for your RPMs?  Do you have any user installed MPI or mpi4py
software around?  If you type:

$ locate mpi

What do you see?  For me this is pretty clearly an installation problem.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 1 October 2016 at 20:14, Mahdi, Sam  wrote:
> Hi Edward,
>
> Oh ok. Thank you for your help, I was able to resolve the problems I had
> with both proteins, and now they are both running. Since there is symmetry
> within the dimer, both chain A and chain B will give me the same S^2 results
> correct?

Hi Sam,

That depends.  If you superimpose A and B and have an RMSD of
0.0, then the S2 values will be identical.  But if
the docking software changed the monomer structures slightly so the
RMSD is not exactly zero, then the S2 values will be slightly
different for some residues.  You can use relax to superimpose
structures and determine the RMSD to very high precision, if you like,
but I'll leave that to you as a learning exercise ;)

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 30 September 2016 at 23:42, Mahdi, Sam  wrote:
> Hi Edward,
>
> So when I ran it as read_mol=0, it gave me the same error. But it worked
> once I changed it to read_mol=1. I thought mol=0 was for set A and mol=1 was
> for set B?

Sorry, I just remembered that the molecule numbering starts from 1.
So read_mol=1 gives chain ID A and read_mol=2 gives chain ID B.  I
should add a check for this argument.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

On 30 September 2016 at 19:45, Mahdi, Sam  wrote:
> Sorry, I just want to make sure I fully understand this so I can explain it
> to my PI:

No problems, this is by far the most complicated aspect in the field of NMR ;)


> So if there is symmetry, I can upload the same pdb file with the dimer (set
> A and B) but tell it to read only one set.

Load rather than upload, but yes.


> Since S^2 isn't effected too much
> versus a dimer versus a monomer, the only thing that is important is the
> change in co-ordinates of one set of the dimer (i.e. the differnence in
> co-ordinates between set A in a monomer, and set A in a dimer co-ordinates,
> or set A in a different version of that dimer's co-ordinates).

S2 is not affected by the reference frame.  This only matters for
comparing diffusion tensors.  Though you will only ever see one
tensor, as that is what is in your NMR sample (if you have a
monomer-dimer mix, then you're in trouble and will see a lot of
artificial Rex and ns motions).


> I say this
> because I have already run my protein's data with the pdb structure of the
> monomer, and I have 2 different pdb files the docking program gave back for
> the dimer (2 different ways the dimer could form from one interface).

Well, your analysis will always return the same diffusion tensor.  If
you want these diffusion tensors to all be in the same frame, use the
relax structure.superimpose user function with the method='fit to
first' argument.  Then just pick which will be your reference
structure and superimpose.  You can superimpose A and B - separately -
onto the monomer frame.

Let's pick the monomer as the reference frame.  Then:

- If you superimpose "dimer 1, struct A" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 1, struct B" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 2, struct A" to the monomer, you
should find the same tensor.
- If you superimpose "dimer 2, struct B" to the monomer, you
should find the same tensor.

If the docking program did not optimise the internal monomer
structure, you will get identical results.  Otherwise you'll see minor
internal motion changes.  If your PI was hoping that you would be able
to tell him that you have a monomer or one of the 2 dimers in your NMR
tube, well then you will need to start to read many, many papers on
diffusion tensor prediction.  But know that all prediction methods
underestimate the diffusion tensor (e.g. David Case is working on this
exact problem for MD simulations).  In this case, relaxation data is
not the best NMR method for this.  It would be better to use RDCs from
a purely steric alignment and to compare that to what PALES prediction
comes up with (though that itself is still a very rough and imperfect
method).

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:47, Mahdi, Sam  wrote:
> I get the same results with the full path mpirun -np 5 ~/relax-4.0.2/relax
> --multi="mpi4py" -v
> Still no output.

The reason is because either OpenMPI or mpi4py are not working.  If
you compiled OpenMPI, then you'll have to compile mpi4py against that
self-compiled version of MPI.  Having multiple versions of MPI on the
system might be problematic, unless you know how to set your
environmental variables correctly for compilation and linking.  If you
cannot run the mpi4py demo that comes with the mpi4py source code,
then you do not have it set up correctly.  If you need help setting up
mpi4py for Python, please see the "Discussion and Support" section at
https://pythonhosted.org/mpi4py/ .  I don't think anyone on the relax
mailing lists have experience with broken mpi4py installations and can
help you fix this.

Regards,

Edward

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Re: relax-users Digest, Vol 116, Issue 38

[Edward d'Auvergne]

Hi Sam,

Please see below:

> I'm a bit confused to that. If the protein is a dimer, and the tumbling
> decreases, will that not results in altered  relaxation data?

Yes.

> Won't the
> relaxation data average be higher, since it is relaxing slower due to its
> increased size (tumbler slower in solution=slower relaxation back to
> equilibrium)?

No.  R2 will be higher.  R1 could go anywhere.  The NOE may not be
affected too much, but it may decrease (maybe).  You need to
understand how the diffusion tensor affects the J(w) spectral density
curves to understand how R1 and the NOE will be affected.


> Also, doesn't S^2 take into account the overall shape of the
> molecule (as well as tensor type) in it's calculations?

No.  The S2 value is the internal motions of the residue.  It is 100%
independent of the global tumbling.


> So won't a dimer
> versus a monomer change the results just due to that?

Not at all.  The optimised diffusion tensor should change, and the S2
value stay the same.


> So should I input both, read_mol=0 and read_mol=1?

No, only one.  You can, however, perform a second analysis later with
read_mol=1 (for comparison).


> So
> structure.read_pdb(file='cluster1_12.pdb', dir=None,
>  read_mol=None, set_mol_name='hRGS4',
> read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None, verbosity=1,
> merge=False)
> So mol_num=0 will be for chain A and mol_num=1 for chain B?

This will have the same IndexError as before - relax will not handle
two identical molecules in a model-free analysis at the same time.
Again, this theory simply does not exist.  So I haven't added it to
relax.  You need to perform the analysis on a single monomer of the
homodimer.  But please check for symmetry - if you don't have
symmetry, nobody on the planet can currently analyse non-symmetric
homodimer data.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:12, Mahdi, Sam  wrote:
> Hi Edward,
>
> So I ran the the mpirun commands you suggested. The echo world works fine. I
> get the same results you did. For the relax one, this is the output I
> recieved
>  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
> Usage: relax [options] [script_file]
>
> RelaxError: incorrect number of arguments

Have a close look at my original text:

[edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
--multi="mpi4py" -v
relax 4.0.2
[edward@localhost ~]$

Note how "relax 4.0.2" is on a different line - that is the relax
output, not the command line input.  Try again without that text.


> RelaxError: ambiguous option: --v (--verification-tests, --version?)

This is because the double-dash to single-dash conversion is only in
the HTML version of the relax manual, and not emails.  Run "relax -h"
to see a description of this option.


> Also, the reason its ./relax is because I have relax 2.2.5 installed, and I
> have that set up as an Alias, so if I just type relax, it'll open up relax
> 2.2.5. So I went to the actual relax-4.0.2. directory instead of indicating
> its path and just typed ./relax. (By I, I mean the administrator of this
> computer, I do not have root access to this computer).

You should set your alias to the relax-4.0.2 version instead.  The
2.2.5 version is very, very old, and many bugs have been fixed since
then.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 19:03, Mahdi, Sam  wrote:
> Hi Edward,
>
> So the GUI problems came from relax 2.2.5 The actual output is big, so I
> will only post where the errors started
> relax> monte_carlo.error_analysis()
>
> relax> results.write(file='devnull', dir='pipe_name', compress_type=1,
> force=True)
> Opening the null device file for writing.
> Traceback (most recent call last):

[snip]

> "/usr/local/Relax/relax-2.2.5/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py",
> line 121, in 
> print("A:\n" % cdp.align_tensors[0])
> TypeError: not all arguments converted during string formatting

[snip]

> That was for relax 2.2.5

These issues were fixed a long, long time ago ;)


> This is the output for relax 4.0.2 It seemed to run and finish, but it gave
> a bunch of errors that stated
> (python:28738): IBUS-WARNING **: Create input context failed: Timeout was
> reached.
>
> This warning basically takes up the entire terminal. Followed by this

These issues are with your Ibus input system, which I guess you have
set up for a few Indian languages on top of English, interacting with
wxPython (again a Fedora configuration issue).  Those are wxPython
messages which are not related to relax.  You should run the wxPython
demos and see if you can type with different Ibus languages, and see
if you get these same Ibus warnings.  No need to report back here
about that though - it would be of more benefit to report this
upstream to Fedora.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 17:37, Mahdi, Sam  wrote:
> Hi Edward,
>
> I also wanted to add, for running a multi-processor platform problem. I
> installed openmpi from the fedora package list, not from the site itself. I
> installed both openmpi, mpi4py, and the openmpi devel. I did not modify
> anything. I can also successfully open relax using mpirun in a single
> processor mode (as in I can load the module, and do mpirun relax and it'll
> work). Do I actually have to do some modifications to openmpi for relax? The
> other computer I was able to successfully run multi-processor on, already
> had openmpi installed and set up, so I only downloaded mpi4py on that
> computer. So I don't know what their setting or configuration was.

Hi Sam,

This sounds like a Fedora OpenMPI misconfiguration.  I guess on the
computer that you see no output with relax, you would also see no
output with:

[edward@localhost ~]$ mpirun -np 5 echo "hello"
hello
hello
hello
hello
hello
[edward@localhost ~]$

In any case, this has nothing to do with relax.  And without a local
login to your computer, there is not much anyone can do about it.  Do
you have a system administrator there who can help you?  Oh, another
good and quick test is:

[edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
--multi="mpi4py" -v
relax 4.0.2
[edward@localhost ~]$

You should only see a single version number printed.  This tests both
your OpenMPI configuration and the mpi4py Python package.  If you do
not see these exact same results, you have some configuration work in
front of you ;)

Regards,

Edward

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Re: Issue in ModelFree Calculation

[Edward d'Auvergne]

On 26 August 2016 at 18:25,   wrote:
> Hi Edward,
> Thank you for your suggestions. Extremely sorry for my late reply. I already
> tried what Troel had told me. As I didn't install the SciPy package (not
> required for ModelFree analysis), I am unable to perform the full test
> suite. As per your suggestion, I went through the wxPython demo, and found a
> missing link of a library package which I have successfully rebuild. Now
> wxPython is setup correctly. But still I get the same error like previous:
>
> terminate called after throwing an instance of 'std::bad_alloc'
>   what():  std::bad_alloc
> Abort (core dumped)
>
> This time I didn't get errors with the libraries. I have also attached the
> output of "$relax -i". Kindly suggest something to resolve this problem.

Hi Aritra,

Did you work out how to correctly install wxPython in the end?  I have
never seen this std::bad_alloc when using different wxPython versions
for almost a decade, so I cannot really help you debug your private
wxPython software installation.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 30 September 2016 at 01:35, Mahdi, Sam  wrote:
> Also, Congrats to Edward!

Thanks :)

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 28 September 2016 at 22:44, Mahdi, Sam  wrote:
> Hey Troels,
>
> I ran the relax -x and recieve this error at the GUI tests
> =
> = GUI tests =
> =
>
> **
> Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort: assertion
> failed: (r == n_visible_rows)
> Abort (core dumped)
> crowlab: [~/relax-4.0.2]>

That is a strange error, but it shouldn't effect you.  It is a minor
problem with your wxPython setup and GTK+ on your system.  It's only
an issue if you are running the GUI and the GUI suddenly crashes on
you.  But again, this problem is not due to relax.

Regards,

Edward

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Re: Using multi-processor for model_free

[Edward d'Auvergne]

On 28 September 2016 at 20:32, Troels Emtekær Linnet
 wrote:
> If you get different results, for the same setup, this is not good.
> Not at all !

Hi,

Sorry for not being more involved, I've been in what could be called
paternity leave.  This point is very, very important.  With the same
setup you must absolutely always obtain the same result.  There are
numerical precision differences between operating systems, CPU types,
and Python 2 vs. 3, but this should be very small.

Regards,

Edward

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Re: Using multi-processor for nmr relax

[Edward d'Auvergne]

On 30 August 2016 at 17:08, Mahdi, Sam  wrote:
> Hi Edward,
>
> Thanks for the quick reply. In the "Further Details" section that shows the
> email archive. When Dr. Thompson is setting up the code to run relax in a
> multi-processor mode he uses the commands "lamboot" and "lamhalt". From what
> I could find, these are commands from the lam/mpi program and not open mpi.
> I know in the manual in "usage of the multi-processor" page, it shows the
> open mpi command "mpirun", but that is the only indication I've seen of
> using open mpi to start relax in multi-processor mode.

I think the old mpi4py can handle these older MPI implementations as
well.  Anyway, you only need that "mpirun" command.

Regards,

Edward

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Re: Using multi-processor for nmr relax

[Edward d'Auvergne]

On 30 August 2016 at 02:57, Mahdi, Sam  wrote:
> Hello everyone,
>
> I was looking to attempt to run relax on a multi-processor platform. I was
> looking at Gary Thompsons overview, and I realized it uses lam/mpi format
> which is no longer provided. I've decided to use it's replacement, open
> mpi. Is there any updated overview that uses open mpi? One that shows a
> step by step guide for how to setup relax to run on multi-processors (with
> commands and outputs showed).

Hi Sam,

Gary Thompson's multi-processor system is based on OpenMPI.  Please see:

http://www.nmr-relax.com/manual/The_multi_processor_framework.html

Which instructions are you referring to?

Regards,

Edward



>
> Thank you
> Sam
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Re: Troubleshooting model-free analysis

[Edward d'Auvergne]

On 8 August 2016 at 21:04, Mahdi, Sam  wrote:
> Hi, I had some general questions regarding model-free analysis that came up
> as I was running it. About 2 months ago, I ran model-free on a 126 residue
> protein. The pdb file I used for the protein had an extra 7 residue
> modifier at one of the terminals, which made it 133 residues; thus, my data
> did not match the pdf file. That run took a little over a week, with the
> sphere model running about 2 models, along with every other model being
> about 2. The data for this run I obtained was unusable (values as small as
> 5x10^-30 for S^2). I attributed this to the fact that my pdf files sequence
> did not align with my data.

Do you mean that the residue numbers were out by 7?  I have considered
this, but relax currently has no way of renumbering the residues in a
3D structure or renumbering the residues of the input data.  So
unfortunately you'll either have to use a molecular view to change
your PDF file, or a script or spreadsheet to renumber your input data.


> I adjusted my relax data (simply added 7 residues with no values), and ran
> it again (all settings the same as before, everything automatic).

I don't think that your data will match up to the correct residues.
The residue numbers in the PDB file and the input relaxation data must
be exact matches.

> This time
> it has taken almost a month, with the sphere model on its 20th run. I saw
> in a previous email that the max is 30 iterations. Is it normal to hit the
> max? Does this mean my data is bad if it requires the max 30 iterations?
> Also, why is it running up to 20 now? The 7 residues I added didn't have
> data, so it doesn't run models for them. I assumed there would be a
> difference in time since the data is now attributed to different spins, but
> not this much of a difference.

If the 3D info and input data do not match, then the results for
non-isotropic (ellipsoidal and spheroidal diffusion) will make no
sense.  In relax you should never need to add relaxation data for
these 7 residues, as relax will handle this situation automatically.
What does your input relaxation data look like?

Regards,

Edward

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Re: error in final execution of NOE in relax

[Edward d'Auvergne]

On 24 June 2016 at 06:49, Rakesh Sharma  wrote:
> Dear all,
>
> I am getting an error in final step of NOE which is the "execution" step.
> the error reads as follows:
>
> Traceback (most recent call last):
>   File "gui/analyses/execute.py", line 87, in run
> self.run_analysis()
>   File "gui/analyses/auto_noe.py", line 378, in run_analysis
> NOE_calc(pipe_name=self.data.pipe_name,
> pipe_bundle=self.data.pipe_bundle, file_root=self.data.file_root,
> results_dir=self.data.save_dir, save_state=False)
>   File "auto_analyses/noe.py", line 90, in __init__
> self.run()
>   File "auto_analyses/noe.py", line 105, in run
> self.interpreter.minimise.calculate()
>   File "prompt/uf_objects.py", line 225, in __call__
> self._backend(*new_args, **uf_kargs)
>   File "pipe_control/minimise.py", line 102, in calc
> api = return_api()
>   File "specific_analyses/api.py", line 133, in return_api
> from specific_analyses.noe.api import Noe
> ImportError: No module named api
>
>
> I have loaded my ref and sat files and when i  try to execute i am getting
> this error every time.
> basic informations:
> I have used all files from test suite itself.
> and the loaded spins are from a structure file 172 spin system
> every step same as mentioned in program noe.py  or manual gui.
>
> if anyone can help me please reply .
> waiting for your reply.

Hi Rakesh (or Akshay?),

Sorry for the late reply, I have been quite busy over the last two
months and have been unable to reply to any messages.  For this error,
which version of relax are you using?  And which operating system are
you running on?  What do you see when you run:

$ relax -i --tee log

This error is quite strange, as the file that cannot be imported
should exist on the system:

[edward@localhost relax-trunk]$ ls specific_analyses/noe/api.py
specific_analyses/noe/api.py

Can you run the test suite?  The following should give zero errors:

$ relax --test-suite --tee tests.log

From the error itself, this simply means that the file
specific_analyses/noe/api.py is missing.  Are you sure your downloaded
relax distribution file is not corrupt?  Does the md5sum value match
the published value:

http://www.nmr-relax.com/download.html

Regards,

Edward

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Re: Troubleshooting model-free analysis

[Edward d'Auvergne]

Hi Sam,

Welcome to the relax mailing lists.  Sorry for the late reply, I've
been quite busy for the last two months.  Please see below:

On 2 July 2016 at 02:41, Mahdi, Sam  wrote:
> I had 2 questions regarding the relax model-free analysis.
> 1: When uploading a pdb file for the spin system, is there a certain way to
> have some residues spins ignored?

I guess you mean reading the spin system from a PDB file.  You can do
this when running the structure.load_spins user function via the
spin_id parameter:

http://www.nmr-relax.com/manual/structure_load_spins.html

Or you can do this afterwards, either using the deselect.spin or
spin.delete user functions:

http://www.nmr-relax.com/manual/deselect_spin.html
http://www.nmr-relax.com/manual/spin_delete.html

> i.e. give it a certain range. E.g. The
> structural data for the pdb file I want uses an extra linker at the
> C-terminus of my protein that is about 7 residues long. The relaxation data
> I have however is for the protein without those 7 extra residues (thus
> residue 7 for the pdb file is residue 1 for my relaxation data). Is there a
> way I can get the relax program to ignore the first 7 residues?

If this is a model-free analysis, the residues without data will be
automatically deselected prior to optimisation (you'll see this in the
logs).

> I tried
> typing in the range I wanted (residue 8 to residue 133 inputed as [8-133])
> in the molecule number to read option, but when I did that, it gave me this
> error RelaxError: No PDB file has been loaded. When I removed the range, it
> uploaded the file but with all the residues, including the linker I didn't
> want.

Ah, I think you might be confusing the loading of a structural file
and the creation of NMR-active spin systems.   All atoms of the
structural file will be loaded into relax, but none of these atoms
will be set a spin systems.  You then have to use the
structure.load_spins user function to pick our the NH atoms pairs of
interest.


> 2: The relaxation data I have is for the backbone (NH), thus the values I
> have for the backbone are for that bond. The pdb file I uploaded has both
> of their spins. The relaxation data I have is one value for each residue
> (for the NH bond). So I assumed that value is the same for both the
> Nitrogen and Hydrogen spin of that residue. E.g. If residue 3 has a R1
> value of 1.03, I assume the nitrogen spin and hydrogen spin both have an R1
> value of 1.03.

This is not correct.  The proton relaxation values will be very
different.  Note that almost no one collects this data as the proton
spin cannot be considered as isolated.  Therefore the normal
assumptions for a model-free analysis of an isolated two spin system
do no hold.  E.g. spin diffusion is an important effect in protons.
This is also why carbon relaxation and model-free analyses are only
performed at natural abundance, to ensure that the system is isolated.

> When I upload the relaxation data with the Nitrogen @N spin
> id string it works fine, each residue has the proper value. However, the
> value for the hydrogen is 0 for each residue.  I tried to create a new data
> set, this time with the spin id string for Hydrogen using the same R1 file
> I had used for the nitrogen, but when I did this I was given this error:
> RelaxWarning: The sequence data in the line ['Residue', 'R1', 'Error'] is
> invalid, the residue number data 'Residue' is invalid.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
> error data is missing.
> Traceback (most recent call last):
>   File "/usr/local/Relax/relax-2.2.5/gui/wizard.py", line 163, in _apply
> self.exec_status = self.on_execute()
>   File "/usr/local/Relax/relax-2.2.5/gui/uf_objects.py", line 867, in
> on_execute
> return_status = self.execute(self.name, **kargs)
>   File "/usr/local/Relax/relax-2.2.5/gui/uf_objects.py", line 797, in
> execute
> return_status = interpreter.apply(uf, *args, **kwds)
>   File "/usr/local/Relax/relax-2.2.5/gui/interpreter.py", line 112, in apply
> apply(fn, args, kwds)
>   File "/usr/local/Relax/relax-2.2.5/generic_fns/relax_data.py", line 1033,
> in read
> pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
> res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
> spin_names=spin_names, spin_id=spin_id)
>   File "/usr/local/Relax/relax-2.2.5/generic_fns/relax_data.py", line 870,
> in pack_data
> new_id = new_ids[0]
> IndexError: list index out of range

You should simply not load any data for the proton.  Then the analysis
will 

Re: Issue in ModelFree Calculation

[Edward d'Auvergne]

On 20 July 2016 at 16:02, Troels Emtekær Linnet  wrote:
> Hi.
>
> Did you compile relax yourself?
> Try compiled version of relax.
>
> Have you tried running the systemtests?
> http://wiki.nmr-relax.com/Installation_test
>
> It looks like you are running mpirun.
> Try running without.
>
> Or look here:
> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing
>
> http://wiki.nmr-relax.com/OpenMPI#Relax_In_multiprocessor_mode
>
> 2016-07-20 15:18 GMT+02:00 :
>
>> Dear all,I am a new user of Relax and I am trying to perform ModelFree
>> calculation with a 207 residue protein using both fully automated and
>> manual protocol of Relax GUI mode. But every time the calculation is
>> stopped with a "bad_alloc" error. The details of the is as follows:
>> terminate called after throwing an instance of 'std::bad_alloc'what():
>>  std::bad_alloc*** Process received signal ***Signal: Aborted (6)Signal
>> code:
>>  
>> (-6)[0x2e040c]/lib/libc.so.6(abort+0x17a)[0xb415ea]/usr/lib/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x167)[0x65c0397]/usr/lib/libstdc++.so.6(+0x57f226)[0x65be226]/usr/lib/libstdc++.so.6(+0x57f263)[0x65be263]/usr/lib/libstdc++.so.6(+0x57f3a2)[0x65be3a2]/usr/lib/libstdc++.so.6(_Znwj+0x87)[0x65be937]/usr/lib/libstdc++.so.6(_ZNSbIwSt11char_traitsIwESaIwEE4_Rep9_S_createEjjRKS1_+0x79)[0x65b35a9]/usr/lib/libstdc++.so.6(_ZNSbIwSt11char_traitsIwESaIwEE9_M_mutateEjjj+0x51)[0x65b5471]/usr/lib/libstdc++.so.6(_ZNSbIwSt11char_traitsIwESaIwEE15_M_replace_safeEjjPKwj+0x3b)[0x65b562b]/usr/lib/libstdc++.so.6(_ZNSbIwSt11char_traitsIwESaIwEE6assignEPKwj+0x5f)[0x65b56ef]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x3a535)[0x1fc8535]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x40714)[0x1fce714]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x7c1bd)[0x200a1bd]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x7c38f)[0x200a38f]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x83a3f)[0x2011a3f]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x98d24)[0x2026d24]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x3f03e)[0x1fcd03e]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(_ZNK16wxStyledTextCtrl7SendMsgEiml+0x2f)[0x1fae5ff]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(_ZN16wxStyledTextCtrl17SetSelectionStartEi+0x34)[0x1fb0f34]/usr/local/lib/libwx_gtk2u_stc-3.0.so.0(+0x33dd4)[0x1fc1dd4]/usr/lib/python2.6/site-packages/wx-3.0-gtk2/wx/_core_.so(+0x10a489)[0x10b0489]/usr/lib/libpython2.6.so.1.0(PyCFunction_Call+0x148)[0x2d77218]/usr/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x499f)[0x2dd475f]/usr/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x85d)[0x2dd63fd]/usr/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x48de)[0x2dd469e]/usr/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x85d)[0x2dd63fd]/usr/lib/libpython2.6.so.1.0(PyEval_EvalFrameEx+0x48de)[0x2dd469e]/usr/lib/libpython2.6.so.1.0(PyEval_EvalCodeEx+0x85d)[0x2dd63fd]/usr/lib/libpython2.6.so.1.0[0x2d63397]***
>> End of error message
>> ***--mpirun
>> noticed that process rank 0 with PID 15605 on node madhava exited on signal
>> 6
>> (Aborted).--
>> So kindly suggest some details about the error and suggest specific hints
>> to resolve the problem.Thanks in advance.
>> Aritra BejDoctoral FellowCSIR - IICB

Hi Aritra,

Did you get a change to look at Troels' suggestions?  Do you see this
error when you run the test suite?  To me this looks like a faulty
installation of wxPython.  These errors and the files listed have
nothing to do with relax.  What is your output when you run:

$ relax -i

Can you run the wxPython demo or the wxPython tests to make sure this
is set up correctly?

Regards,

Edward

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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

On 3 June 2016 at 12:08, Edward d'Auvergne <edw...@nmr-relax.com> wrote:
> Hi Petr,
>
> For the new bug report at https://gna.org/bugs/?24675, now looking at
> the results I can see that this is actually quite a deliberate
> feature.  For reference, I will attach the plots for residues 133 and
> 134 for the CR2 model as a PDF file to that bug report
> (disp_CKIRD_133_N.pdf and disp_CKIRD_134_N.pdf).  For residue 133,
> there the blue line can be seen to be the dispersion curve predicted
> for the missing 600 MHz data.  For 134, the green line is the
> predicted dispersion curve for the 950 MHz data.
>
> The R20 values come from the fitting of the single field strength data
> points, and this value is independent of field strength.  So the
> predicted curves are perfectly correct - they are exactly where they
> are supposed to be.  Assuming the model to be correct, the predicted
> curves are what the real data should look like.  So the curves without
> measured data are actually quite powerful tools for investigating why
> the data is missing.  They are also useful for investigating how well
> the model fits to single field strength data.  It is also quite easy
> in Grace to double click on the curve and hide it, if desired.
> Therefore I think I'll leave the plotting code as it is.

Hi Petr,

Sorry, the R20 values are field strength dependent, but both are fit
during the optimisation of the dispersion models with missing data.
This is problematic as one parameter is undefined - the R20 for the
missing field - and this interferes with optimisation algorithms.  The
undefined R20 value can float around to any value, and this breaks the
rules that most algorithms absolutely rely on.  Hence the solution
found is unlikely to be the minimum in the optimisation space.  I
would therefore suggest deselecting these spins for now, as the
results are nonsensical.  It might take me a while to update each part
of relax to detect the missing data for one entire field strength from
the N fields, and drop back to N-1 fields.  This bug might take a
while to fix!  I might have to spend a few days working on that one
next week.

Regards,

Edward

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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

Hi Petr,

For the new bug report at https://gna.org/bugs/?24675, now looking at
the results I can see that this is actually quite a deliberate
feature.  For reference, I will attach the plots for residues 133 and
134 for the CR2 model as a PDF file to that bug report
(disp_CKIRD_133_N.pdf and disp_CKIRD_134_N.pdf).  For residue 133,
there the blue line can be seen to be the dispersion curve predicted
for the missing 600 MHz data.  For 134, the green line is the
predicted dispersion curve for the 950 MHz data.

The R20 values come from the fitting of the single field strength data
points, and this value is independent of field strength.  So the
predicted curves are perfectly correct - they are exactly where they
are supposed to be.  Assuming the model to be correct, the predicted
curves are what the real data should look like.  So the curves without
measured data are actually quite powerful tools for investigating why
the data is missing.  They are also useful for investigating how well
the model fits to single field strength data.  It is also quite easy
in Grace to double click on the curve and hide it, if desired.
Therefore I think I'll leave the plotting code as it is.

Cheers,

Edward



On 2 May 2016 at 17:37, Edward d'Auvergne <edw...@nmr-relax.com> wrote:
> On 29 April 2016 at 11:58, Petr Padrta <pad...@ncbr.muni.cz> wrote:
>> On Wed, Apr 27, 2016 at 11:27:09AM +0200, Edward d'Auvergne wrote:
>>> On 22 April 2016 at 20:43, Petr Padrta <pad...@ncbr.muni.cz> wrote:
>>> > Hi Edward,
>>> >
>>> > OK,  I finally managed to create a bug report on gna with attached 
>>> > example.
>>>
>>> Hi Petr,
>>>
>>> Thank you for that.  For reference, the report is at
>>> https://gna.org/bugs/?24601 .  I have taken your data and script and
>>> created the following relax system test:
>>>
>>> $ relax -s Relax_disp.test_bug_24601_r2eff_missing_data
>>>
>>> I used this to catch the bug you saw and to fix all the issues.  Note
>>> that it took a bit longer than normal as the first error you saw was
>>> only one of 3.  I also had to update the Monte Carlo simulation error
>>> analysis code, and the Grace plotting code.  I have committed the
>>> changes:
>>>
>>> http://article.gmane.org/gmane.science.nmr.relax.scm/25955
>>>
>>> When using this, please carefully check that all is working as
>>> expected.  The system test now passes, however there might be other
>>> strangeness (for example, check your Grace graphs for incorrect data
>>> labels).  For any other issues you see, if you could create a separate
>>> bug report for each, that would be appreciated.  As before, if you
>>> could include truncated data and a script to replicate the issue, that
>>> would be much appreciated as I could then create the system test to
>>> help fix the problem.  The more bugs reported - from critical to
>>> superficial - the smoother we can make the analysis process!  Even
>>> confusing text messages by relax deserve a report.
>>>
>>> For obtaining the code, if you need this soon, I would suggest
>>> directly obtaining it from the source code repository:
>>>
>>> http://www.nmr-relax.com/download.html#Source_code_repository
>>>
>>> The reason is because there are a few newly introduced bugs that I
>>> would like solved before we release relax 4.0.2.  So it might take a
>>> few weeks before the new release is out.
>>>
>>> Regards,
>>>
>>> Edward
>>
>> Hi Edward,
>>
>> Thanks! I fetched last SVN version (r28204) and so far it seems that your new
>> dispersion code works as expected. The (rhetorical) question is what to do 
>> with
>> interpolated dispersion curves from missing B0 fields - they have the right
>> shape but are shifted along R2eff-axis as their r20 is unknown. Hmm, I can
>> always delete them from the grace plots. Or maybe I'll do another bug report
>> after some more testing.
>
> Hi Petr,
>
> A new bug report for such things would be much appreciated.  I can
> then list the bugs one after the other and their details in the
> release notes.  It also makes it incredibly easy for a developer to
> fix the bug if truncated, minimal data sets and a script and/or
> instructions are attached to the bug report.  That way a system test
> can be quickly constructed to reproducibly capture the bug.  In most
> cases where a system test can be set up, the fix then only requires
> 5-10 minutes to resolve.
>
> Cheers,
>
> Edward

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Re: Data files

[Edward d'Auvergne]

Hi Rakesh,

As Troels mentioned, the test suite directories contain a huge number
of examples.  A good one is the OMP data from Gitti et al. (2005), in
test_suite/shared_data/model_free/OMP (see my PhD thesis at
https://minerva-access.unimelb.edu.au/handle/11343/39174 ).
Alternatively, you could download data from the BMRB.  You can then
follow the tutorials for model-free analyses from the relax manual:

The new protocol in the prompt/script UI mode - (
http://www.nmr-relax.com/manual/The_new_protocol_in_the_prompt_script_UI_mode.html
)
The new protocol in the GUI - (
http://www.nmr-relax.com/manual/The_new_protocol_in_the_GUI.html )

You will have to play around with the starting steps, as setting up
spin systems can take two major routes - from a PDB file (with atomic
coordinates), or from a text file containing your primary sequence (no
positional information, but loading the positions from a PDB file
later).  I hope this helps.

Regards,

Edward



On 29 May 2016 at 21:12, Troels Emtekær Linnet  wrote:
> Hi Rakes.
>
> Look in the test_suite folder.
>
> Hundreds of unit and system test is provided there.
>
> Best
> Troels
>
> 2016-05-27 14:21 GMT+02:00 Rakesh Sharma :
>
>> Hi everyone,
>> can anybody have idea that from where to get data files used in relax
>> manual calculations. I am new to relax and learning it. I get structure
>> file from protein data bank for molecule used in relax and learned up to
>> spin loading. Now for further analysis i need sparky list files for T1, T2
>> and Noe. Does anybody has idea that from where i can get these and  process
>> with same as in manual.
>> Regards,
>> Rakesh Sharma
>>
>> <
>> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
>> >
>> Virus-free.
>> www.avast.com
>> <
>> https://www.avast.com/sig-email?utm_medium=email_source=link_campaign=sig-email_content=webmail
>> >
>> <#DDB4FAA8-2DD7-40BB-A1B8-4E2AA1F9FDF2>
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Re: missing data in relaxation dispersion

[Edward d'Auvergne]

On 29 April 2016 at 11:58, Petr Padrta <pad...@ncbr.muni.cz> wrote:
> On Wed, Apr 27, 2016 at 11:27:09AM +0200, Edward d'Auvergne wrote:
>> On 22 April 2016 at 20:43, Petr Padrta <pad...@ncbr.muni.cz> wrote:
>> > Hi Edward,
>> >
>> > OK,  I finally managed to create a bug report on gna with attached example.
>>
>> Hi Petr,
>>
>> Thank you for that.  For reference, the report is at
>> https://gna.org/bugs/?24601 .  I have taken your data and script and
>> created the following relax system test:
>>
>> $ relax -s Relax_disp.test_bug_24601_r2eff_missing_data
>>
>> I used this to catch the bug you saw and to fix all the issues.  Note
>> that it took a bit longer than normal as the first error you saw was
>> only one of 3.  I also had to update the Monte Carlo simulation error
>> analysis code, and the Grace plotting code.  I have committed the
>> changes:
>>
>> http://article.gmane.org/gmane.science.nmr.relax.scm/25955
>>
>> When using this, please carefully check that all is working as
>> expected.  The system test now passes, however there might be other
>> strangeness (for example, check your Grace graphs for incorrect data
>> labels).  For any other issues you see, if you could create a separate
>> bug report for each, that would be appreciated.  As before, if you
>> could include truncated data and a script to replicate the issue, that
>> would be much appreciated as I could then create the system test to
>> help fix the problem.  The more bugs reported - from critical to
>> superficial - the smoother we can make the analysis process!  Even
>> confusing text messages by relax deserve a report.
>>
>> For obtaining the code, if you need this soon, I would suggest
>> directly obtaining it from the source code repository:
>>
>> http://www.nmr-relax.com/download.html#Source_code_repository
>>
>> The reason is because there are a few newly introduced bugs that I
>> would like solved before we release relax 4.0.2.  So it might take a
>> few weeks before the new release is out.
>>
>> Regards,
>>
>> Edward
>
> Hi Edward,
>
> Thanks! I fetched last SVN version (r28204) and so far it seems that your new
> dispersion code works as expected. The (rhetorical) question is what to do 
> with
> interpolated dispersion curves from missing B0 fields - they have the right
> shape but are shifted along R2eff-axis as their r20 is unknown. Hmm, I can
> always delete them from the grace plots. Or maybe I'll do another bug report
> after some more testing.

Hi Petr,

A new bug report for such things would be much appreciated.  I can
then list the bugs one after the other and their details in the
release notes.  It also makes it incredibly easy for a developer to
fix the bug if truncated, minimal data sets and a script and/or
instructions are attached to the bug report.  That way a system test
can be quickly constructed to reproducibly capture the bug.  In most
cases where a system test can be set up, the fix then only requires
5-10 minutes to resolve.

Cheers,

Edward

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Re: regarding installation

[Edward d'Auvergne]

On 20 April 2016 at 12:39, Rakesh Sharma  wrote:
>
> Thanks for your reply. I am not able to run relax so not able to generate log 
> file. I Downloaded relax then put that in system path by using my computer as 
> told in manual. I have python 2.7.11 Numpy 1.11.0, Relax is 4.0.1. Can you 
> please tell me the procedure after installing python how to install that in 
> window. I can download other version of python and all software. When I 
> started installing, I got problem with cythonize then when I rectify that 
> then with numpy now it is showing some error with code at line 59 and 72 in 
> dep-chk.py when i am typing relax in cmd. Please tell me step wise 
> installation procedure so that I can check I followed the right path or not.

Hi,

Are you using the official Python from http://python.org ?  If not,
then that is very likely to be your problem.  Can you run Python, and
type "import numpy"?  Does this show any error messages?

Regards,

Edward

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Wiki spam bot cleanup.

[Edward d'Auvergne]

Hi,

If no one objects, I might clean up - i.e. permanently delete - all
non-trusted users on the relax wiki:


http://wiki.nmr-relax.com/index.php?title=Special:ListUsers==500

There are a large number of spam bots sitting there that are blocked
from doing anything, and it would be good to clear them out.  If you
have an account but are not trusted yet, unlikely as most of the
non-trusted users have typical spam bot names, please respond to this
email to have your wiki account trusted.

To improve the wiki user registration process, I have installed the
customUserCreateForm extension:

http://wiki.nmr-relax.com/index.php?title=Special:UserLogin=signup
https://www.mediawiki.org/wiki/Extension:CustomUserCreateForm

Well, more like manually created the extension.  I have included a new
text section:

"""
Editing the wiki

To be granted editing access to the relax wiki, please send a message
to the http://www.nmr-relax.com/communication.html#relax-users;>relax-users
mailing list. This is to verify that you are not a spam bot
automatically creating an account. Please include a link to your
research group's website, or equivalent, to help with the verification
process. This measure was taken due to excessive and uncontrollable
spamming of the wiki.
"""

This should significantly clarify the process.

Regards,

Edward

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Re: How to make one fit from two experiments.

[Edward d'Auvergne]

Hi Jens,

Welcome to the relax mailing lists!  For you question, you may need to
be more specific about which type of experiment, as relax can analyse
data from many different unrelated NMR experiments.  Not only that,
but there are many different types of dynamics analysis that can be
performed on the same data.  For a full list, see:

http://www.nmr-relax.com/features.html

As for how to use relax, I would suggest looking at the relax manual.
For many of the analyses, you'll find step-by-step tutorials for using
relax either via the more commonly used scripting interface, or for
some analyses via the graphical user interface (GUI).  These should
help you get started, and will be sufficient for most analyses.  I
hope this helps.  Don't hesitate to ask if you have any other
questions.

Regards,

Edward




On 18 December 2015 at 12:20, Jens Fuglsang Ringsholm
 wrote:
> Hello
> i am an undergrad student trying to use relax for fitting two experiments 
> with the same protein, at different field strengths. Does relax have an 
> application for this and how do i use it?
>
> Jens Fuglsang Ringsholm
> ___
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Re: Experimental: Try relax at Google Cloud Computing

[Edward d'Auvergne]

On 29 November 2015 at 00:46, Troels Emtekær Linnet
 wrote:
> Hi relax users.
>
> I have written a tutorial to get relax running at Google Cloud Computing.
>
> The tutorial can be found here:
> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing
>
> Consider this as a very experimental procedure.
>
> The Cost of running Google Cloud Computing has been rapidly dropping in
> 2015.
>
> This could be of interest to have access to 32 cores for a limited time, if
> some computations should be performed fast, and no immediately computer
> cluster is available at your facility.
>
> Any comments, hints or tips is appreciated.
>
> Is this a viable and sustainable solution?

Hi Troels,

This sounds like quite a useful service if someone would like to run a
heavy calculation on a cluster when they don't have access to powerful
computing infrastructure.  The instructions at
http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing are very
useful for setting this up.  I would advise though to first run the
calculation on a single core system as a test, to make sure everything
is running smoothly.  The user should carefully check every single
warning.  That would avoid running an incorrectly set up calculation
on the Google Cloud Computing, so that the user doesn't have to re-run
all the calculations a second time.  I think this is quite a good
idea!

Cheers,

Edward

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Re: model free analysis: spin deselection problem

[Edward d'Auvergne]

On 19 November 2015 at 13:03, Alain Oregioni  wrote:
> Hi Edward,
>
> Thanks for your reply. I was out of the office till now, so I've not had
> time to debug more till now.
>
>  I had a look at the log and I didn't see any warning earlier than the ones
> I mentioned, so I'm again stuck. I will check for name mismatch though, as
> this has happened before.
>
> Sorry about the attachments, I'm afraid I didn't read the communication
> protocols...Here's the beginning of the script:
>
> #
>
> # The diffusion model.
> DIFF_MODEL = 'prolate'
>
> # The model-free models.  Do not change these unless absolutely necessary,
> the protocol is likely to fail if these are changed.
> MF_MODELS = ['m0', 'm1', 'm2', 'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
> LOCAL_TM_MODELS = ['tm0', 'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7',
> 'tm8', 'tm9']
>
> # The grid search size (the number of increments per dimension).
> GRID_INC = 13
>
> # The optimisation technique.
> MIN_ALGOR = 'newton'
>
> # The number of Monte Carlo simulations to be used for error analysis at the
> end of the analysis.
> MC_NUM = 500
>
> # Automatic looping over all rounds until convergence (must be a boolean
> value of True or False).
> CONV_LOOP = True
>
> # The local paths.
> SEQ_PATH =
> 'C:\\Users\\aoregio\\Desk\\Crick\\Projects\\Woolfson_coiledCoil\\RC'
>
>
> # Set up the data pipe.
> ###
>
> # The following sequence of user function calls can be changed as needed.
>
> # Create the data pipe.
> pipe_bundle = "mf (%s)" % asctime(localtime())
> name = "origin - " + pipe_bundle
> pipe.create(name, 'mf', bundle=pipe_bundle)
>
> # Load the PDB file.
> structure.read_pdb('4DZM-CC-pIL-I17N-dimer-AsnA.pdb', dir='.',
> set_mol_name=['CCDi_mol1','CCDi_mol2'], alt_loc='A')
>
> # Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
> #structure.load_spins(spin_id='@N', ave_pos=False)
> structure.load_spins(spin_id=':6@N', ave_pos=False)
> structure.load_spins(spin_id=':13@N', ave_pos=False)
> structure.load_spins(spin_id=':17@N', ave_pos=False)
> structure.load_spins(spin_id=':20@N', ave_pos=False)
> structure.load_spins(spin_id=':27@N', ave_pos=False)
>
> spin.isotope('15N', spin_id='@N*')
> spin.isotope('1H', spin_id='@H*')
>
> # Generate the 1H spins for the magnetic dipole-dipole relaxation
> interaction.
> sequence.attach_protons()

Hi Alain,

The problem is right here!  The sequence.attach_protons user function
is only for use when you don't have a 3D structure
(http://www.nmr-relax.com/manual/sequence_attach_protons.html).  I
should probably document that better!  Ok, done:

http://article.gmane.org/gmane.science.nmr.relax.scm/25823

You should load your protons from the 3D structure with
structure.load_spins user function calls
(http://www.nmr-relax.com/manual/structure_load_spins.html).  That way
the proton spin containers will have atomic coordinates, and the NH
bond vectors can then be calculated (which you'll need to add to your
script, see http://www.nmr-relax.com/manual/interatom_unit_vectors.html).
For more details, see:


http://www.nmr-relax.com/manual/d_Auvergne_protocol_script_mode_setting_up_the_spin_systems.html

and the following pages.  If you do not have protons in your PDB file,
you'll need to generate them with external software (Molmol, Pymol,
etc.).  Unfortunately I haven't implemented a structure.attach_protons
user function yet, as I never found the citation for an algorithm to
correctly place protons in an X-ray structure.  And I know that the
calculated positions are not always the same for different software
programs, so it would be good to implement a number of the algorithms
so that there is a choice.

Regards,

Edward

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Re: model free analysis: spin deselection problem

[Edward d'Auvergne]

On 12 November 2015 at 19:00, Alain Oregioni  wrote:
> Hi,
>
> I'm new to Relax and I'm having some trouble running a model free analysis
> with my data. In short, all the spins are being deselected, supposedly
> because of missing structural data even though I have loaded a PDB of the
> structure.
>
> Some details of the system:
> I'm using Relax 4.0.0 with scripts under Win7 Pro 64
> The molecule is a homodimer and I have R1, R2, hetNOE data at 600 and 700
> MHz
> The data is only from 5 spins out of 31 (for a chain, both chains being
> identical)
> The pdb is from a crystal structure (so, no proton)
>
> What I've done so far:
> I've run the dauvergne_protocol.py with 'local_tm' and 'sphere' without
> problem. 'sphere' converged after 5 rounds. Both gave 'aic' solutions (but
> then, I think they are not using the PDB directly).
>
> However, when I run any of 'prolate', 'oblate', 'ellipsoid', the script end
> up with "no model selected...'aic' pipe not created".
> Looking at the console output, it seems that after the data is loaded fine
> and dAuvergne_protocol() starts:
> - pipe is created OK
> - local_tm is read OK
> - model_free.remove_tm() is run OK
> - diffusion_tensor.init() is run OK
> - fix()  is run OK
> Then:
> - minimise.grid_search() starts and deselects all the spins: "Over-fit spin
> deselection... because of missing structural data"
> Of course, after this, the grid search does not work.
>
> I'm thinking that my system is far from standard for this type of analysis,
> and there are a few possibilities for things going wrong, starting with the
> fact it's a homodimer, and that the spins with data are in limited numbers
> (although they are spatially well distributed). But I have no ideas
> how/where/why, so I'm a bit stuck for now. Does anyone have an idea?
>
> I've attached a screenshot and the first 3 scripts in case that helps. If
> you need anything else, please ask.


Hi Alain,

Welcome to the relax mailing lists!  Have you managed to work out what
the problem was?  I would suggest looking at your log file (you should
really run relax with the --log or --tee options to capture
everything).  Look at the very top of the log for any warnings.  This
type of error is almost always visible as a warning in the set up
stage of the analysis.  Specifically where the structural data is
loaded into the relax data store.  There is probably a mismatch
between the X and H spins and how they are named in the PDB file.
What are the first few lines of your analysis script?

Note that attachments cause a large strain on the open source
infrastructure, as they are amplified and sent off to everyone on the
mailing list and to the 4 mailing list archives (
http://www.nmr-relax.com/communication.html#relax-users ).  Therefore
attachments will be automatically stripped out of the mailing list
messages.  To send files, the best is to create a bug report (
https://gna.org/bugs/?group=relax ) or support request (
https://gna.org/support/?group=relax ) and attach the files there.


> I've also noticed something that's probably not related, but just in case:
> it seems that the function minimise.grid_search() starts with 'inc=11' even
> if I passed 'GRID_INC=13' in my script (through dAuvergne_protocol() )...If
> it's not expected, and other variables are somehow not updated, this might
> be the cause of the problems.

If you have a look at the auto_analyses/dauvergne_protocol.py file (
http://www.nmr-relax.com/api/4.0/auto_analyses.dauvergne_protocol-module.html
), you see another option called 'diff_tensor_grid_inc' which defaults
to {'sphere': 11, 'prolate': 11, 'oblate': 11, 'ellipsoid': 6}.  This
is where this number of 11 comes from.  See the file itself for more
details.

Regards,

Edward

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Re: back calculation of relaxation data

[Edward d'Auvergne]

On 5 November 2015 at 15:53, Edward d'Auvergne <edw...@nmr-relax.com> wrote:
> On 5 November 2015 at 14:05, Christina Möller <c.moel...@fz-juelich.de> wrote:
>> I know that the relaxation data can also be back calculated using the
>> equations 7.3a - 7.8 in the relax manual (PDF), although it is not that
>> trivial for an ellipsoid model because I need to determine the weights. Is
>> there a reason why you define c=1/3(ωH*∆σ)^2 (eq. 7.5) instead of
>> c=2/15(ωN*∆σ)^2 like it can be found in literature?
>
> These two factors come from using CGS vs. SI units.  I have mentioned
> this issue before (see
> http://thread.gmane.org/gmane.science.nmr.relax.devel/1023/focus=1034
> ).  I have also started a stub wiki article to help explain these
> differences - http://wiki.nmr-relax.com/CGS_versus_SI . In SI units
> the correct unit (squared) is (ω·∆σ)^2 / 3, and SI units are used
> throughout relax.  This has made some parts of relax more difficult to
> implement as there are many equations in the literature in CGS units,
> and the authors will often not identify this older system.  Some
> stubborn people just prefer the magnetic constant to be 1 rather than
> µ0/(4π), and will not shift from the CGS metric system to the SI
> metric system.

Hi Christina,

The wiki article http://wiki.nmr-relax.com/CGS_versus_SI is now
somewhat improved.  However it doesn't cover all of the NMR constants
yet, as that will be a lot of work to derive.  Anyway, I hope that
helps a little to understand the equation differences seen in the NMR
literature.

Regards,

Edward

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Re: back calculation of relaxation data

[Edward d'Auvergne]

Hi Christina,

Please see below:

On 5 November 2015 at 14:05, Christina Möller  wrote:
> Dear Edward and relax-users,
>
> I am sorry to ask you again for some advice to back calculate the relaxation
> data from the model parameter values. Here is what I tried so far:
> For the back calculation I loaded the final results determined by the
> automated analysis using the dauvergne_protocol.py into the relax gui. Then
> I selected the back_calc tool from user functions -> relax_data.
> After starting the back calculation without any entry
> relax> relax_data.back_calc(ri_id=None, ri_type=None, frq=None)
> I get the following error message:
> RelaxWarning: comparison to `None` will result in an elementwise object
> comparison in the future.

This is a warning produced by more recent versions of the numpy Python
package.  It is harmless message about changes which will occur in
numpy, and it is safe to ignore.  Note that I have fixed this in the
source code repository and the fix will appear in the future when I
release relax 4.0.1 (it is not present in relax 4.0.0 at
http://wiki.nmr-relax.com/Relax_4.0.0 ).  This was first reported at:

[relax-users] RelaxWarning: comparison to `None` will result in an
elementwise object comparison in the future (
http://thread.gmane.org/gmane.science.nmr.relax.user/1839 ).

And the solution at:

[relax-users] Re: RelaxWarning: comparison to `None` will result
in an elementwise object comparison in the future (
http://thread.gmane.org/gmane.science.nmr.relax.user/1844 ).


> If I put the frequency in
> relax> relax_data.back_calc(ri_id=None, ri_type=None, frq=599468076.0)
> I get another error message
> Traceback (most recent call last):
>  File
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/gui/interpreter.py",
> line 306, in run
>fn(*args, **kwds)
>  File
> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/pipe_control/relax_data.py",
> line 132, in back_calc
>spin.ri_data_bc[ri_id] = api.back_calc_ri(spin_index=spin_index,
> ri_id=ri_id, ri_type=ri_types[ri_id], frq=frqs[ri_id])
> KeyError: 'R1_600'
>
> Can you give me a hint what I am doing wrong?

I would suggest using the sample_scripts/model_free/generate_ri.py
sample script.  The relax_data.back_calc user function requires that
the relaxation data ID, the relaxation type, and frequency arguments
be supplied to correctly calculate the desired data (see
http://www.nmr-relax.com/manual/relax_data_back_calc.html ).  Without
this information, relax cannot determine what you would like to do.
Using the sample script would be the easiest option.


> I know that the relaxation data can also be back calculated using the
> equations 7.3a - 7.8 in the relax manual (PDF), although it is not that
> trivial for an ellipsoid model because I need to determine the weights. Is
> there a reason why you define c=1/3(ωH*∆σ)^2 (eq. 7.5) instead of
> c=2/15(ωN*∆σ)^2 like it can be found in literature?

These two factors come from using CGS vs. SI units.  I have mentioned
this issue before (see
http://thread.gmane.org/gmane.science.nmr.relax.devel/1023/focus=1034
).  I have also started a stub wiki article to help explain these
differences - http://wiki.nmr-relax.com/CGS_versus_SI . In SI units
the correct unit (squared) is (ω·∆σ)^2 / 3, and SI units are used
throughout relax.  This has made some parts of relax more difficult to
implement as there are many equations in the literature in CGS units,
and the authors will often not identify this older system.  Some
stubborn people just prefer the magnetic constant to be 1 rather than
µ0/(4π), and will not shift from the CGS metric system to the SI
metric system.

Regards,

Edward

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Re: RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future

[Edward d'Auvergne]

On 16 October 2015 at 17:42, Sze Chan  wrote:
> Hello Edward,
>
> The problem to load into @N* appears when I use my full data, but using a 
> truncated version does not cause a problem.
>
> I attached, the truncated data, full data, and the PDB I've been using (its a 
> truncated version of a PDB from the RCSB) in the bug report.

Cheers!  I've create a system test and now fixed the problem in relax.
See https://gna.org/bugs/?23933#comment3 .  The problem was introduced
in Nov. 2014.  It might take me a while to release a new version of
minfx, bmrblib, and relax to have all these issues resolved.  Anyway,
you can ignore the comparison to 'None' warnings, as these are
harmless for now.  And they are fixed in minfx, bmrblib, and relax and
so will be part of relax 4.0.1.  With the fixes, the relax log will
look like:


"""
relax> pipe.create(pipe_name='mf', pipe_type='mf', bundle=None)

relax> structure.read_pdb(file='LARA_N_term_no_helixFH_reg.pdb',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids',
read_mol=None, set_mol_name=None, read_model=None, set_model_num=None,
alt_loc=None, verbosity=1, merge=False)

Internal relax PDB parser.
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/LARA_N_term_no_helixFH_reg.pdb'
for reading.
Adding molecule 'LARA_N_term_no_helixFH_reg_mol24' (from the original
molecule number 24).

relax> structure.load_spins(spin_id='@N', from_mols=None,
mol_name_target=None, ave_pos=True)
Adding the following spins to the relax data store.

# mol_name  res_numres_namespin_num
spin_name
LARA_N_term_no_helixFH_reg_mol24329GLN 1
N
LARA_N_term_no_helixFH_reg_mol24330GLN 10
N
LARA_N_term_no_helixFH_reg_mol24331SER 19
N

relax> structure.load_spins(spin_id='@H', from_mols=None,
mol_name_target=None, ave_pos=True)
Adding the following spins to the relax data store.

# mol_name  res_numres_namespin_num
spin_name
LARA_N_term_no_helixFH_reg_mol24330GLN 0
H
LARA_N_term_no_helixFH_reg_mol24331SER 0
H

relax> structure.load_spins(spin_id='@NE1', from_mols=None,
mol_name_target=None, ave_pos=True)
Adding the following spins to the relax data store.

RelaxWarning: No spins matching the '@NE1' ID string could be found.

relax> structure.load_spins(spin_id='@HE1', from_mols=None,
mol_name_target=None, ave_pos=True)
Adding the following spins to the relax data store.

RelaxWarning: No spins matching the '@HE1' ID string could be found.

relax> relax_data.read(ri_id='R1_600', ri_type='R1', frq=600402816.0,
file='r1_600.txt',
dir='/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids',
spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=2, error_col=3,
sep=None, spin_id=None)
Opening the file
'/data/relax/relax-trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt'
for reading.
Traceback (most recent call last):
  File "/data/relax/relax-trunk/test_suite/system_tests/model_free.py",
line 499, in test_bug_23933_relax_data_read_ids
self.interpreter.relax_data.read(ri_id='R1_600', ri_type='R1',
frq=600402816.0, file='r1_600.txt', dir=path, res_num_col=1,
data_col=2, error_col=3)
  File "/data/relax/relax-trunk/prompt/uf_objects.py", line 225, in __call__
self._backend(*new_args, **uf_kargs)
  File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 925, in read
pack_data(ri_id, ri_type, frq, values, errors,
mol_names=mol_names, res_nums=res_nums, res_names=res_names,
spin_nums=spin_nums, spin_names=spin_names, spin_id=spin_id)
  File "/data/relax/relax-trunk/pipe_control/relax_data.py", line 773,
in pack_data
raise RelaxMultiSpinIDError(spin_ids[i], new_ids)
RelaxMultiSpinIDError: RelaxError: The spin ID
'#LARA_N_term_no_helixFH_reg_mol24:331' corresponds to multiple spins,
including '#LARA_N_term_no_helixFH_reg_mol24:331@N' and
'#LARA_N_term_no_helixFH_reg_mol24:331@H'.
"""


The bug that was hidden from you in the GUI will now stop relax and
pop up a RelaxError dialog.  Therefore you don't need the new relax
version or use a checked out copy of the source code repository
(unless you'd like the new code to remove all of the numpy
FutureWarning messages).  You just need to set the spin_id argument to
'@N'.  This allows relax to understand that you have nitrogen and not
proton relaxation data - relax will accept both and it is currently
ambiguous if it is 'N' or 'H' data.  Anyway, thank you for the bug
report and attached files.  This has allowed me to fix both the numpy
FutureWarning and missing 'ids' variable problems.  If you see any
other strange warnings or errors, it would be appreciated if you could
report them so that they can be resolved for future relax 

Re: RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future

[Edward d'Auvergne]

On 12 October 2015 at 09:04, Edward d'Auvergne <edw...@nmr-relax.com> wrote:
> On 11 October 2015 at 19:32, Sze Chan <samuelsw.c...@mail.utoronto.ca> wrote:
>> Hello,
>>
>>
>> While I was setting up my modelfree analysis in the GUI automated protocol , 
>> I received the error in the controller:
>>
>>
>> RelaxWarning: comparison to `None` will result in an elementwise object 
>> comparison in the future.
>>
>>
>> After loading my data, setting dipolar interactions, setting CSA relaxations 
>> and setting the isotopes but before execution of the analysis.
>>
>>
>> I'm not sure what happened to cause the warning, but when the modelfree 
>> analysis is running, each successive round of optimization in each model 
>> does not compare to the previous round, instead it would always compare each 
>> optimized chi-square value to 'none' such as in round 21 of the oblate model:
>>
>>
>> Storing the optimisation results for the spin 
>> '#LARA_N_term_no_helixFH_reg_mol24:358@N', the optimised chi-squared value 
>> is lower than the current value (283.50425283 < None).
>>
>>
>> Even though I'm guessing it should refer to a previously optimised value?
>>
>>
>> During the analysis it would go through the default 30 rounds of 
>> optimisation for each global model but not reach convergence.
>>
>>
>> I was wondering how I can remedy this or at least create a log file so I can 
>> make my problem more clear.
>
> Hi Sam,
>
> I would suggest running relax with these options:
>
> $ relax --gui --log relax_warning.log --traceback
>
> This will start the GUI, send all output into a 'relax_warning.log'
> file, and produce highly detailed RelaxError and RelaxWarning messages
> pointing to the exact place in the code where the problem occurred.
> Then exit relax once this warning first occurs (using kill if
> necessary).
>
> Which version of relax are you using by the way?  And which numpy
> version?  The RelaxWarning message you see is either due to Python or
> numpy (specifically using newer versions).  I have seen it many times
> before, and I try to avoid it in the code where possible.  Strangely I
> have never seen this one before.  The relax test suite tests the full
> automated dauvergne_protocol analysis, including multiple rounds of
> optimisation and convergence tests.  And for each relax release I run
> the full test suite on Python version 2.5, 2.6, 2.7, 3.0, 3.1, 3.2,
> 3.3, and 3.4 (and now 3.5).  Because the test suite has not replicated
> the problem you see, maybe it has something to do with numpy.  Anyway,
> I look forward to seeing the traceback on that RelaxWarning, and maybe
> the output of 'relax -i'.  If you'd like to attach files, then please
> create a bug report and attach the file to the report (
> https://gna.org/bugs/?func=additem=relax ).

Hi Sam,

Thanks for creating the bug report ( https://gna.org/bugs/?23933 ).
From this I can see that the RelaxWarning is not the problem, but
rather this:

"""
relax> relax_data.read(ri_id='R1_600_2', ri_type='R1',
frq=600402816.0, file='C:\\Users\\Sam Chan\\Desktop\\r1_600.txt',
dir=None, spin_id_col=None, mol_name_col=None, res_num_col=1,
res_name_col=None, spin_num_col=None, spin_name_col=None, data_col=2,
error_col=3, sep=None, spin_id='@N*')
Opening the file 'C:\\Users\\Sam Chan\\Desktop\\r1_600.txt' for reading.
Traceback (most recent call last):
  File "C:\relax\gui\wizards\wiz_objects.py", line 166, in _apply
self.exec_status = self.on_execute()
  File "C:\relax\gui\uf_objects.py", line 917, in on_execute
return_status = self.execute(self.name, **kargs)
  File "C:\relax\gui\uf_objects.py", line 839, in execute
return_status = interpreter.apply(uf, *args, **kwds)
  File "C:\relax\gui\interpreter.py", line 109, in apply
fn(*args, **kwds)
  File "C:\relax\pipe_control\relax_data.py", line 920, in read
pack_data(ri_id, ri_type, frq, values, errors,
mol_names=mol_names, res_nums=res_nums, res_names=res_names,
spin_nums=spin_nums, spin_names=spin_names, spin_id=spin_id)
  File "C:\relax\pipe_control\relax_data.py", line 767, in pack_data
if ids:
NameError: global name 'ids' is not defined
"""

Did you see this error in the GUI?  To help debug this, I was
wondering if you could attach a shortened version of the r1_600.txt
file (truncated to 1 or 2 residues, but still enough to trigger the
error).  I could then use this to create a new system or GUI test to
catch the problem.  That will allow me to come up with a fix in
normally a few minutes.  Oh, you may have seen that I just released
relax 4.0.0, the first of the 4 series (
http://wiki.n

Re: RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future

[Edward d'Auvergne]

On 11 October 2015 at 19:32, Sze Chan  wrote:
> RelaxWarning: comparison to `None` will result in an elementwise object 
> comparison in the future.

Hi Sam,

This warning is due to something called a FutureWarning which was
introduced into numpy >= 1.9.  It looks like the numpy would like to
change how '==' operates on their numpy arrays.  So the previous relax
code was of the form:

if vector == None:

This used to work and was good for checking if we had set a value.
However the numpy people would like us to now instead use:

if vector is None:

I am running the test suite now with Python 3.5 and numpy 1.9.2, using:

$ python3.5 relax -x -d --tee test_suite.log --traceback

That way I can find all such warnings and replace '==' with 'is' and
silence them all.  However as I mentioned in the other email, this is
not the problem you are having with the analysis.  Thanks for pointing
it out though, the fixes I'll make here will allow relax to continue
running with future numpy versions.

Cheers,

Edward

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Re: RelaxWarning: comparison to `None` will result in an elementwise object comparison in the future

[Edward d'Auvergne]

On 11 October 2015 at 19:32, Sze Chan  wrote:
> Hello,
>
>
> While I was setting up my modelfree analysis in the GUI automated protocol , 
> I received the error in the controller:
>
>
> RelaxWarning: comparison to `None` will result in an elementwise object 
> comparison in the future.
>
>
> After loading my data, setting dipolar interactions, setting CSA relaxations 
> and setting the isotopes but before execution of the analysis.
>
>
> I'm not sure what happened to cause the warning, but when the modelfree 
> analysis is running, each successive round of optimization in each model does 
> not compare to the previous round, instead it would always compare each 
> optimized chi-square value to 'none' such as in round 21 of the oblate model:
>
>
> Storing the optimisation results for the spin 
> '#LARA_N_term_no_helixFH_reg_mol24:358@N', the optimised chi-squared value is 
> lower than the current value (283.50425283 < None).
>
>
> Even though I'm guessing it should refer to a previously optimised value?
>
>
> During the analysis it would go through the default 30 rounds of optimisation 
> for each global model but not reach convergence.
>
>
> I was wondering how I can remedy this or at least create a log file so I can 
> make my problem more clear.

Hi Sam,

I would suggest running relax with these options:

$ relax --gui --log relax_warning.log --traceback

This will start the GUI, send all output into a 'relax_warning.log'
file, and produce highly detailed RelaxError and RelaxWarning messages
pointing to the exact place in the code where the problem occurred.
Then exit relax once this warning first occurs (using kill if
necessary).

Which version of relax are you using by the way?  And which numpy
version?  The RelaxWarning message you see is either due to Python or
numpy (specifically using newer versions).  I have seen it many times
before, and I try to avoid it in the code where possible.  Strangely I
have never seen this one before.  The relax test suite tests the full
automated dauvergne_protocol analysis, including multiple rounds of
optimisation and convergence tests.  And for each relax release I run
the full test suite on Python version 2.5, 2.6, 2.7, 3.0, 3.1, 3.2,
3.3, and 3.4 (and now 3.5).  Because the test suite has not replicated
the problem you see, maybe it has something to do with numpy.  Anyway,
I look forward to seeing the traceback on that RelaxWarning, and maybe
the output of 'relax -i'.  If you'd like to attach files, then please
create a bug report and attach the file to the report (
https://gna.org/bugs/?func=additem=relax ).

Cheers,

Edward






>
>
> Sam
> ___
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>
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> relax-users@gna.org
>
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Re: Model free on symmetric homodimer, problems with grace plots

[Edward d'Auvergne]

On 7 October 2015 at 09:43, Panwalkar, Vineet  wrote:
> Hello Edward and relax users,
>
> I have been recently using relax to carry out model free analyses on two 
> different states of my protein at 600 and 800 MHz. I am working with a LOV 
> domain (132 residues) which exists in a ground "dark" state and a photoactive 
> "light" state. Both states exist as a symmetric homodimer in solution. For 
> the analysis I have been using the crystal structures, one monomer at a time. 
> Also, the resonances showing overlap have not been included in the analyses. 
> There is no difference in the backbone as such between the two crystal 
> structures. Along with model-free I have also carried out reduced spectral 
> density mapping. The J(0)s of both the states agree well between the two 
> fields. Hence there is nothing wrong with the data as such. Also both the 
> J(w) agree well with my het-NOE and R1 with respect to regions in the protein 
> showing fast timescale backbone motion.
>
> The model free analysis of the "dark" state goes fine. The S2 values show 
> same regions having fast timescale motions as observed from the raw 
> relaxation data and rSDM. Both the monomers individually give me 
> approximately comparable results. For e.g., a loop between residues 100 and 
> 110 shows flexibility on fast time scale according to the raw data, rSDM as 
> well as relax S2 values.
>
> However, for the "light" state the results from model free appear quite 
> bizarre for both the monomers. The average S2 for the "dark" state was ~ 0.8. 
> As per my raw data and rSDM, I expected the S2 values to be slightly elevated 
> in "light" state. However, my "light" state S2 values are on an average 0.17! 
> Also the same loop is now with higher than average S2 values in the "light" 
> state whereas the raw data and rSDM showed the loop to be flexible, albeit 
> less flexible compared to the "dark" state. The internal motions (Te) are 
> less than 5 ps and seen only in 7 residues. No Ts or Tf. I have attached 
> figures from the spectral density mapping as well as the "dark" and "light" 
> state S2 values to illustrate better what I am trying to say.
> Also, I repeated the "dark" state model free analysis with "dark" state 
> structures. thinking that there might be some bug somewhere and got results 
> just like earlier. But not with the "light" state. Since the backbones 
> between two states are near identical, I used the "dark" state structure to 
> run with relax on the "light" state data. I again get these bizarre results. 
> I am about to run model free with "light" state structure and "dark" state 
> relaxation data. However, I am not sure where the problem lies, whether it is 
> the structure, my data or some bug somewhere. Since the J(0)s add up nicely, 
> I do not think it is the data. It is unlikely that it is bug since the "dark" 
> state ran fine. It is also unlikely that the structure is strange since dark 
> and light states have near identical backbones and there are no missing 
> residues in either of the structures. I must also add that the correlation 
> time obtained from relax are actually comparable with the ones extracted from 
> R2/R1 ratio for both the "dark" and the "light" states. It is only the motion 
> parameters which are weird for the "light" state.
>
> Has anyone encountered something like this recently? Any help/advice here 
> will be very helpful. At this moment the data is only with two fields but I 
> do plan to run relaxation at 900 MHz and use the three fields for model-free 
> as soon as I get time on the magnet.

Hi Vineet,

One thing you must consider is if the approximation of a single
ellipsoidal diffusion tensor is reasonable for the system.  Sometimes
this is not the case.  For example if the single rigid body assumption
is violated, if the dimerization is not 100%, or there are long
flexible tails (breaking the 'free' rigid body assumption).  If you
have been using the model-free analysis protocol I came up with in:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. ( http://dx.doi.org/10.1039/b702202f )

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133. (
http://dx.doi.org/10.1007/s10858-007-9213-3 )

then there is a good check you can perform.  Compare the final results
to the results of the local tm global model.  The local tm model is
almost always over fit, hence the balance of variance vs. bias will be
tipped in the direction of variance (it will be noisy).  However the
local tm global model will have a lot less bias.  In practical terms,
this means that the model will not be affected by the assumption of a
global diffusion tensor (note that it is 

Re: fixed tm values

[Edward d'Auvergne]

Hi Christina,

Welcome to the relax mailing lists!  As Troels mentioned, I have been
on holidays so can only now reply.  For details, please see below:

On 3 June 2015 at 14:32, Christina Möller c.moel...@fz-juelich.de wrote:
 Dear Edward and relax users,

 I successfully performed the dauvergne_protocol.py analysis scripts to
 determine the ps - ns dynamics of a 14 kDa protein. The global
 correlation time tm is 9.6 ns.

This value does not seem unreasonable.

 Since other methods suggested a smaller
 global correlation time tm,

Which other methods have you used?  You should note the following issues:

- It is well known that MD underestimates the global correlation time
by about half and David Case is actively researching this area.
- Stoke's law and the related hydrodynamic beads model from Garcia de
la Tor are reasonable for estimating tm for isolated molecules.
However with the super high concentration in NMR samples, these tend
to underestimate the tm value by about half as they do not take
micro-viscosity into consideration.
- ORD measurements as well, as the tm changes between the lower
concentration optical spectroscopic sample and the NMR sample by about
a factor of 2 (micro-viscosity effects being a major factor again).


 I would like to know whether it is possible
 to fix the tm value in all rounds of individual model-free
 optimisations?

As Troels pointed out, this is of course possible.  You can take, for
example, the sample_scripts/model_free/diff_min.py script.  This
already implements a lot of what Troels described for you.  Note
however that this needs to be executed iteratively until the global
chi-squared value between iterations is identical.  See figure 2 of:

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models II. A new methodology for the dual optimisation of the
model-free parameters and the Brownian rotational diffusion tensor. J.
Biomol. NMR, 40(2), 121-133. (
http://dx.doi.org/10.1007/s10858-007-9213-3 ).

This global iterative optimisation of the diffusion tensor is
essential, and you'll find it documented in Mandel et al., 1995 as
well as in the papers by the Dasha authors.  It will take between 5-20
iterations to properly converge (in rare cases it can be 2 iterations,
in others 50).  For more details, you really should read:

How to get model free parameters from output files (
http://thread.gmane.org/gmane.science.nmr.relax.user/1375/focus=1378
).

This requires an initial diffusion tensor estimate.  And as I
demonstrated in the above paper - as well as first shown in the
Korzhnev et al., 1999 bacteriorhodopsin fragment paper (
http://dx.doi.org/10.1023/a:1008356809071 ) - if this is too far off,
the global minimum will never be reached.  You can however directly
compare the two results using AIC values (not chi-squared values as
the individual model-free models for each residue will be different
and the effects of parsimony will not be taken into account).  An
additional thread which might be of interest is:

AIC to select diffusion model (
http://thread.gmane.org/gmane.science.nmr.relax.user/885/focus=891 ).

There are plenty of other relax-users mailing list threads on the
subject which you can search for at:

http://dir.gmane.org/gmane.science.nmr.relax.user


 The corresponding chi2 values might then be useful to
 evaluate the global correlation times that I obtained by different methods.

Note that you should compare the chi-squared values from the same
program, just to be sure.  Also note that the spherical angle and
Euler angle notations in Modelfree4, Dasha, Tensor2 and relax are not
compatible.  The problem is that the definitions of these angles are
not documented (except in relax) so if you take a diffusion tensor
from one and input it into another, you will see the angles swing
around wildly with the global iterative diffusion tensor estimate
until it converges to the same tensor but with the different angles
(except when a local minimum is hit).  There are 2406 Euler angle
conventions and symmetries for diffusion tensors!

One last thing to note is that relax is extremely flexible in what it
can do.  Using specially designed scripts, relax can replicate the
results of Modelfree4, Dasha, Tensor2, or DYNAMICS.  One exception is
that relax uses a real optimisation constraint algorithm (the
augmented Lagrangian or method of multipliers,
https://en.wikipedia.org/wiki/Augmented_Lagrangian_method ,
https://gna.org/projects/minfx/ ) which the other model-free softwares
do not, hence there can be cases where relax does not find exactly the
same result as the other softwares.

I hope all this information helps.  You should also consider Troels'
suggestion of the dx.map user function to see the diffusion tensor
parameter space (or 3D subsets of it).  I used this in figure 6 of:

d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR
dynamic models I. Minimisation algorithms and their performance within
the 

Re: using relax on supercomputer

[Edward d'Auvergne]

Hi Lora,

I was wondering if you could resend the message that Troels is talking
about, as it missed the mailing list.  Troels has added a link to
http://thread.gmane.org/gmane.science.nmr.relax.user/1821 to link to
the information you provided, but unfortunately it is absent from the
thread and archives.  To keep the thread structure intact, could you
copy and paste the text and then reply to the original email?  That
will preserve the thread structure in the above link.  Having this
information in the mail archives would be greatly appreciated.

Cheers!

Edward


On 29 May 2015 at 18:55, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Hi Lora.

 Thank you for your detailed message.

 I believe this will help alot of other people, including me. :-)

 I took the liberty to write a little post about on the relax wiki.
 http://wiki.nmr-relax.com/OpenMPI#Setting_up_relax_on_super_computer_Beagle2

 I hope it comes of use for someone.

 Thanks again!

 Best
 Troels


 2015-05-29 11:46 GMT+02:00 Troels Emtekær Linnet tlin...@nmr-relax.com:

 Dear Lora.

 I am interested in achieving the same thing on our small local computer
 cluster.

 I have read from
 http://beagle.ci.uchicago.edu/using-beagle/

 That you use Torque to submit jobs.

 Have you succeeded in getting this to work with relax?

 Best
 Troels



 2015-05-15 19:52 GMT+02:00 Lora Picton lkpic...@uchicago.edu:

 Hi,

 I'm working with the administrators of the super computer on UChicago's
 campus (Beagle2) to get relax running on their system.

 Because of the way that their system is set up, I will need to have my
 data and script files in one directory and submit my job and instructions
 to a queue. I can't use the gui version to implement the full analysis.

 I have two questions about doing this.
 1. Can I use the GUI to set everything up and then instead of starting
 it, save the scripts so that I can direct them to be started in the queue,
 or do I have to modify each script with a text editor?

 2. When starting the full analysis with a script UI mode (which I need to
 do to submit the job), the manual says you need 6 scripts, one for each
 diffusion model. Does this mean that I will need to submit multiple jobs to
 a queue, one for each model? If yes, would the first 5 need to be done
 before the final is used? Or would it be possible to direct all of them
 to occur in one large script?

 Thanks for any input you might have!
 Lora Picton
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Re: Problems Loading PDB

[Edward d'Auvergne]

Hi Dave,

Sorry for the delayed response, I have just returned from holidays.
Please see below:


On 4 June 2015 at 17:02, Lawrence David Finger d.fin...@sheffield.ac.uk wrote:
 I posed these questions some time ago, but I have not heard from anyone or 
 whether my message was accepted by the moderator. I guess I am not on the 
 list. Below is what I wrote initially.

I just checked the mailing list backend, and your d.finger email
address is not present.  You should try subscribing again.  One step
that is often forgotten is that after you receive the subscription
request email and follow the link, you have to in that page
specifically select to subscript or ignore the subscription.  In most
cases when you are not subscribed, the mailing list maintainer Chris
MacRaild will see your message and accept it.  One problem though is
that public mailing lists are a massive magnet for spam.  So if your
message is buried in a pile of 1000 spam messages, it is sometimes not
seen and thrown out with the 1000 junk messages.  Being subscribed to
the list avoids this.


 We have a question concerning our results from our latest calculations using 
 relaxGUI. We have fed the program NMR relaxation data at 500 and 600 MHz on 
 the free protein and a structure of the protein in complex with DNA from an 
 X-ray structure. We know that binding of DNA induces some secondary 
 structures because the free protein has sections missing in the pdb. Because 
 the free protein structure has residues missing presumably due to disorder in 
 the crystal, we chose to use the structure of the bound protein. Could the 
 use of a structure of our protein with more order than expected cause 
 problems with the selection of the rotational diffusion tensor?

Very much so!  If there is a conformational change, you should
probably split the protein in 2 and analyse each domain or rigid body
separately.


 The diffusion tensor the program has selected doesn’t seem to match the 
 overall shape of the protein. If it can cause a problem, how do I add the 
 residues missing from the crystal structure for the refinement? Furthermore, 
 can the program handle some residues missing in crystal structures?

The problem with a non-spherical model-free analysis is that the
average XH bond vector orientation in solution is a core requirement
of the theory.  If this is incorrect, this can lead to either of the
two well known artefacts:

- Artificial nanosecond motions (the Schurr 1994 paper).
- Artificial Rex value (the Tjandra 1995 paper).

See my 2007 Mol. Biosyst. paper at http://dx.doi.org/10.1039/b702202f
for a review about this problem and how this relates to the under or
overestimation of the vector projection within the diffusion tensor.

One way to handle this situation is to use what I have termed a
'hybrid' model.  For residues which have no structural information,
you can use the local tm model and avoid a global correlation time,
and linearly combine these models with the global diffusion tensor
models applied to all known residues.  You could even shift residues
with high beta factors from the global Brownian diffusion model into
the 'local tm' model category.  relax will allow you to do this, but
it will require a bit of manual work.  So if you know you have two
domains with large structural rearrangements, you can perform three
analyses:

- Local tm for missing residues.
- The full protocol for domain 1.
- The full protocol for domain 2.

Then combine the final results as one model.  There should be zero
overlap of residues in these 3 divisions.  You could then compare
this, using AIC values to take parsimony and non-nested model
differences into account, to a local tm model for all residues.  Note
that the local tm models are generally quite noisy if data from  3
fields are used.  I hope this helps.

Regards,

Edward

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Re: using relax on supercomputer

[Edward d'Auvergne]

Hi Lora,

Please see below:

 I have two questions about doing this.
 1. Can I use the GUI to set everything up and then instead of starting it, 
 save the scripts so that I can direct them to be started in the queue, or do 
 I have to modify each script with a text editor?

Yes, just save the state and then create a basic script that loads
that state and then execute the auto-analysis.  You just need a
pipe.create user function call and the last line of the
dauvergne_protocol.py sample script (and an import from the top).  It
can all be done in a 3 line script, if you wish.


 2. When starting the full analysis with a script UI mode (which I need to do 
 to submit the job), the manual says you need 6 scripts, one for each 
 diffusion model. Does this mean that I will need to submit multiple jobs to a 
 queue, one for each model? If yes, would the first 5 need to be done before 
 the final is used? Or would it be possible to direct all of them to occur 
 in one large script?

This is optional for the auto-analysis, see the diff_model argument:

http://www.nmr-relax.com/api/3.3/auto_analyses.dauvergne_protocol.dAuvergne_protocol-class.html#__init__

You should use this documentation to help set up the auto-analysis in
script mode.

Regards,

Edward

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Re: Problems Loading PDB

[Edward d'Auvergne]

Hi Ian,

Welcome to the relax mailing lists!  For this problem, it is just
relax not knowing which of the alternate coordinates in the PDB file
to use.  See altLoc at
http://www.nmr-relax.com/api/3.3/lib.structure.pdb_read-module.html#atom
(this is a copy of the PDB standard).  This is usually only for side
chains anyway, and it is generally safe to set it to 'A'.  It is a
character which starts at 'A', so you will find in column or position
17 of the PDB file 'A' and 'B' for some atoms (sometimes 'C' and even
'D', though more is rather rare).  I have deliberately not set the
default to 'A', just in case someone encounters a file with alternate
coordinates.  Then you can look at the PDB file and determine which,
if any, of the coordinates should be used.  For a model-free analysis,
if altLoc is set for the backbone N or H, deselecting the residue
might be the best strategy.  But it is up to you to determine what the
best approach for this PDB file is.  If you have any other issues,
please don't hesitate to ask!

Regards,

Edawrd


On 27 April 2015 at 19:16, Ian A Bennet iabenn...@sheffield.ac.uk wrote:
 Hello,

 We are new relax users and are struggling to load structural information
 for each residue.  We have tried loading a pdb file (attached) generated by
 Pymol after proton addition, however we get this error:

 RelaxError: Multiple alternate location indicators are present in the PDB
 file, but the desired coordinate set has not been specified.

 When we set the alternate location indicator to any number (I have no
 clue which number it should be set to) it says the structure is loaded, but
 when trying to extract the atomic positions it spits out an error about no
 positional information could be found.

 Is there some sort of easy format that PDB files should be in so that relax
 can extract the information from them?

 Many thanks,

 Ian.
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Re: Help with setting up relax files

[Edward d'Auvergne]

Hi Sam,

For relax, you simply input the peak lists.  Using the
spectrum.read_intensities user function
(http://www.nmr-relax.com/manual/spectrum_read_intensities.html), you
can load in peak intensities - either height or volumes - from many
different spectral software programs.  This includes Sparky, XEasy,
NMRView, NMRPipe seriesTab, and a generic column formatted text file
(the Bruker Dynamics Centre format is also supported).  relax is
designed so that users never have to perform format conversions to
input or output data.  If a format conversion is necessary, I would
insist on a new support request being created and an example data file
attached to it.  Then the support for the format can be quickly added
to relax (by first implementing system tests).

The problem with conversions is the chance of data loss or a mistake
being made.  But the conversions in relax are all extensively and
repeatedly checked via the comprehensive test suite, so that you can
be sure that no mistakes are made:

$ relax --test-suite --time

But just with all other analysis software, you should always be on the
look out for problems, as all software contains bugs.  So software can
be treated as a black box, but always be vigilant and sceptical of all
results.  Oh, thanks to advances implemented by Troels, you can now
simultaneously load all peak lists with one spectrum.read_intensities
user function call.  This is especially useful if you are using the
GUI.

Regards,

Edward




On 26 February 2015 at 23:58, Sze Chan samuelsw.c...@mail.utoronto.ca wrote:

 Hello,

 Currently, I'm collecting more NMR data so I haven't had much time to analyze 
 the data.

 Usually, I extract the raw peak heights at each CPMG Hz for each residue 
 (assignments saved in my ccpnmr project) so I don't have a peaklist for my 
 CPMG data. The same is done for my fast time scale dynamics (T1/T2/NOE).

 So I was wondering if there was a way to set up the files in a tabular format 
 by hand? (an example of such a table would be very helpful). I was hoping if 
 there was some way to fit my dispersion data just on a per residue basis, 
 similar to how another NMR program, NESSY, takes in data.

 Thank you for your time and patience, as an undergrad a lot of the 
 information and navigation is quite overwhelming so its great to have some 
 help!

 Regards,
 Sam
 
 From: edward.dauver...@gmail.com edward.dauver...@gmail.com on behalf of 
 Edward d'Auvergne edw...@nmr-relax.com
 Sent: Thursday, February 26, 2015 12:32 PM
 To: Troels Emtekær Linnet
 Cc: Sze Chan; relax-users@gna.org
 Subject: Re: Help with setting up relax files

 Hi Sam,

 I was wondering if you still had problems with the loading of peak
 heights for relaxation dispersion in relax?  It should be pretty
 flexible and handle most formats you throw at relax.  If you have a
 peak list format that is not supported, it would be appreciated if you
 could create a support request (https://gna.org/support/?group=relax,
 https://gna.org/support/?func=additemgroup=relax).  If you attach a
 truncated peak list to the request, slightly randomised if you would
 like to keep the data private, then that file could be used to quickly
 implement support for the format.

 Cheers,

 Edward




 On 15 February 2015 at 10:58, Troels Emtekær Linnet
 tlin...@nmr-relax.com wrote:
 Hi Sam.



 Try to have a look on the wiki:
 http://wiki.nmr-relax.com/Category:Tutorials

 http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_cpmg_fixed_time_recorded_on_varian_as_fid_interleaved

 Maybe you can figure out something.

 If you need more help.

 Make a suppert request
 https://gna.org/support/?group=relax

 Upload an example peak list for each CPMG frq.
 Make a file, listing filename for peaklist and corresponding CPMG frq.

 You need to determine the error of your experiments.
 If you have peak heights which are replicate/triplicate, then this is fine.
 Or else you need to measure RMSD of the noise in the spectrum.

 What is also:
 Relaxation dispersion CPMG constant time delay T (in s).
 The NMR field strength of the spectrum. (750 MHz ?)

 Best
 Troels


 2015-02-15 1:09 GMT+01:00 Sze Chan samuelsw.c...@mail.utoronto.ca:

 Hello all,


 I am an undergrad that is new to the field of NMR and I was hoping to get
 some basic help in setting up my data for analysis.


 For my CPMG relaxation dispersion experiments, I usually process my data
 through NMR pipe and then extract the peak heights through ccpnmr with each
 plane as the CPMG frequency. In the end for each residue, I get the peak
 height at various CPMG frequencies.


 However, I'm not sure how to format my table or know what software I can
 use to format my data so that I can input it into relax. If anyone has any
 help, I'd greatly appreciate it since I'm very new to the field and all the
 analysis that comes with it.


 Regards,

 Sam


 Department of Biochemistry - University of Toronto

Re: If I can run modelfree analysis using relaxation data from only single magnetic field?

[Edward d'Auvergne]

Hi Danyun,

Welcome to the relax mailing lists!  Hopefully the wiki link that
Troels sent you will be sufficient.  Note that there is a huge amount
of information in the links to previous discussion threads at
http://wiki.nmr-relax.com/Model-free_analysis_single_field#The_Question
which may answer many other questions you might have.  I have also
added this email thread
(http://thread.gmane.org/gmane.science.nmr.relax.user/1800) to the
wiki page for future reference.

Regards,

Edward


On 28 January 2015 at 09:47, Troels Emtekær Linnet
tlin...@nmr-relax.com wrote:
 Hi Danyun Zeng.

 Try have a look on this wiki page:
 http://wiki.nmr-relax.com/Model-free_analysis_single_field

 Best
 Troels

 2015-01-28 1:13 GMT+01:00 Danyun Zeng zeng...@hotmail.com:

 Hi, all,

 I'm new to relax. I want to use it for modelfree analysis recently and I
 only have a set of relaxation data from 500MHz NMR spectrometer.
 May I ask if I can run modelfree analysis using relaxation data from only
 single magnetic field? All the sample scripts in relax's manual requires
 data at least from 2 fields. I haven't find a way to do that.
 I heard ModelFree4 can do it. But that software is kind of old, and I have
 to separately calculate r1 r2 noe. That's why I still want to try relax
 first. If anyone can teach me, I really appreciate!

 Best regards,
 Danyun

 Postdoctoral fellow

 Department of Biochemistry  Biophysics
 Texas AM University
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Re: Error calculation of individual parameter dw from MC

[Edward d'Auvergne]

Hi Troels,

I guess this is for a clustered analysis?  Would you be able to create
a system test which demonstrates this problem?  Two spins with two or
three MC simulations would be sufficient.  The code you've identified
in the specific_analyses.relax_disp.api.sim_return_param() function
should work, as the spin index si comes from the
param_index_to_param_info() function.  If anything, it is that
function in the specific_analyses/relax_disp/parameters.py file which
does not correctly find the spin index, and that function uses the
relaxation dispersion loop_parameters() function to identify the
parameter.  From the code, I don't see any problems:

http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.api-pysrc.html#Relax_disp.sim_return_param
http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.parameters-pysrc.html#param_index_to_param_info
http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.parameters-pysrc.html#loop_parameters

Cheers,

Edward

On 14 January 2015 at 13:42, Troels Emtekær Linnet tlin...@gmail.com wrote:
 If I do it for the first spin:

 cdp.mol[0].res[0].spin[0].dw_sim

 import numpy as np

 a = np.array([0.9451997476845593, 0.8054522239552819, 0.9277366066500237,
 0.9625036075584432, 0.8802059033496906, 0.9972921559805459,
 0.8743682211305104, 0.9500671171775412, 0.9155241775057494,
 0.9468124355863968, 0.96417019553941, 1.0170148731646576,
 0.808583141857603, 0.9101215951359578, 0.950865223270674,
 1.0307772448494004, 0.8993891518585049, 0.9139606433668193,
 0.956733004106492, 0.8978513006468936, 0.9453834676054009,
 0.910827776695774, 0.8808826708447804, 0.9260230255021042,
 0.9502172231153962, 0.86537440977864, 0.8859323973019857,
 0.8893764312486083, 0.9731605295027338, 1.0041329485057724,
 0.9484007034626689, 0.8562407086263037, 0.8949760705986323,
 0.9494159177232087, 0.9536607612740096, 0.981423499818791,
 0.8795248912995862, 0.9703162419092174, 0.9498731423252795,
 0.8766210928540752, 0.8716559260505473, 0.9697324548237327,
 0.8330252500434963, 0.9463453433710509, 0.8936136907056889,
 0.9393334443985975, 0.9310091998291463, 0.9409086436225335,
 0.9194230869394555, 0.9150169906828444, 0.937755163159723,
 0.821586577578577, 0.8844807208799657, 0.9509710398156324,
 0.9244476893902771, 0.8912100177428832, 0.8667907082691229,
 0.8523582565296183, 0.911207452505568, 0.8546152190640066,
 0.8797463442344267, 0.932394336758319, 0.965515026672257,
 0.8967984708313228, 0.9562847792473697, 0.9662836189055034,
 0.9187032714923455, 0.9552991998159039, 0.8721372679559742,
 0.951677098087865, 0.970701220083394, 0.880277858875798,
 0.8868837879487532, 0.8289936757848054, 0.8452643978000389,
 0.8608520989786752, 0.9408859834978103, 0.9477671884481794,
 0.9355182739828974, 0.9058402170229929, 0.888170996310456,
 0.8872799805467638, 0.872024994152445, 0.8802787599729809,
 0.9527566512472332, 0.8864763874519584, 0.8436371510886024,
 0.9828573401629994, 0.9771419297773668, 0.906019424908,
 0.9707157553507724, 0.879689193482642, 0.9436375392843368,
 0.9927180210208233, 0.9267041637380232, 0.9412299434835303,
 0.926346676233505, 0.8774254634406635, 0.8826805167518188,
 0.8865687070701256, 0.9512379465525047, 0.9641813779931143,
 0.953277273069755, 1.0047488071722177, 0.8521615788684946,
 0.8680916457728691, 0.9340561986882852, 0.9477037339014749,
 0.9469454099421577, 0.9005897924118794, 0.8803998440278067,
 0.9024692253200567, 0.909122984887152, 0.8399468552579564,
 0.9571308078096232, 0.9683939646310176, 0.9419649402214831,
 0.9613040120941247, 0.9781781986426726, 0.9805816556476108,
 0.94937687356695, 0.960693374108915, 0.9530824549428941,
 0.8843910508664925, 0.8945735422767003, 0.9049315573495563,
 0.8802084472126279, 0.8328713211676385, 0.9406572364992218,
 0.910325290850831, 0.9318781551216802, 0.8934350965988851,
 0.8353799932488288, 0.951313819820305, 0.855414485205892,
 0.909767822028357, 0.8924203614902587, 0.9408505916987862,
 0.8751269857340623, 0.938822046542, 0.9499696867836579,
 0.9605708328530759, 0.9054195520491586, 0.8859714100727238,
 0.9305256454920723, 0.937758620326129, 0.9320519159136575,
 0.9656009544636446, 0.9584255887448183, 0.8738507316066699,
 0.9661737748832995, 0.8717799481773607, 0.959731591608098,
 0.9640387155993229, 0.8600096309525227, 0.8762991916520275,
 0.9329290121054334, 0.838440295115923, 0.8399242891708862,
 0.8145405034437483, 0.961537851810333, 0.9430802765990043,
 0.9358230046912992, 0.9359556594347389, 0.9553690216306725,
 0.9943161816393639, 0.9823102347443102, 0.9586429773877578,
 0.9599901351410914, 0.9229179343561751, 0.9481274587922217,
 0.8970870418193109, 0.9940991138386224, 0.8321641241392229,
 0.820820360597734, 0.9239612738883967, 0.8028677971498746,
 0.9470524563800362, 0.8770948453727446, 0.8786234926518741,
 0.9500563596927654, 0.9425646627827216, 0.9813509472882151,
 0.8963925974037248, 0.9665748645186323, 0.9481002238259164,
 0.9762925493355714, 0.9448903713592451, 0.8703265705873551,
 

Re: Error calculation of individual parameter dw from MC

[Edward d'Auvergne]

Hi,

Ok, I can now see that the lines

if not param_name in ['r2eff', 'i0']:
si = 0

could be a problem.  The 'not' part should probably not be there!
This code was introduced at:

http://article.gmane.org/gmane.science.nmr.relax.scm/17945

Once this important bug is fixed (https://gna.org/bugs/?23186), and
the relax test suite still passes, I'll make a new relax 3.3.5 release
(http://wiki.nmr-relax.com/Category:Release_Notes).

Cheers,

Edward



On 14 January 2015 at 14:05, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Hi Troels,

 I guess this is for a clustered analysis?  Would you be able to create
 a system test which demonstrates this problem?  Two spins with two or
 three MC simulations would be sufficient.  The code you've identified
 in the specific_analyses.relax_disp.api.sim_return_param() function
 should work, as the spin index si comes from the
 param_index_to_param_info() function.  If anything, it is that
 function in the specific_analyses/relax_disp/parameters.py file which
 does not correctly find the spin index, and that function uses the
 relaxation dispersion loop_parameters() function to identify the
 parameter.  From the code, I don't see any problems:

 http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.api-pysrc.html#Relax_disp.sim_return_param
 http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.parameters-pysrc.html#param_index_to_param_info
 http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp.parameters-pysrc.html#loop_parameters

 Cheers,

 Edward

 On 14 January 2015 at 13:42, Troels Emtekær Linnet tlin...@gmail.com wrote:
 If I do it for the first spin:

 cdp.mol[0].res[0].spin[0].dw_sim

 import numpy as np

 a = np.array([0.9451997476845593, 0.8054522239552819, 0.9277366066500237,
 0.9625036075584432, 0.8802059033496906, 0.9972921559805459,
 0.8743682211305104, 0.9500671171775412, 0.9155241775057494,
 0.9468124355863968, 0.96417019553941, 1.0170148731646576,
 0.808583141857603, 0.9101215951359578, 0.950865223270674,
 1.0307772448494004, 0.8993891518585049, 0.9139606433668193,
 0.956733004106492, 0.8978513006468936, 0.9453834676054009,
 0.910827776695774, 0.8808826708447804, 0.9260230255021042,
 0.9502172231153962, 0.86537440977864, 0.8859323973019857,
 0.8893764312486083, 0.9731605295027338, 1.0041329485057724,
 0.9484007034626689, 0.8562407086263037, 0.8949760705986323,
 0.9494159177232087, 0.9536607612740096, 0.981423499818791,
 0.8795248912995862, 0.9703162419092174, 0.9498731423252795,
 0.8766210928540752, 0.8716559260505473, 0.9697324548237327,
 0.8330252500434963, 0.9463453433710509, 0.8936136907056889,
 0.9393334443985975, 0.9310091998291463, 0.9409086436225335,
 0.9194230869394555, 0.9150169906828444, 0.937755163159723,
 0.821586577578577, 0.8844807208799657, 0.9509710398156324,
 0.9244476893902771, 0.8912100177428832, 0.8667907082691229,
 0.8523582565296183, 0.911207452505568, 0.8546152190640066,
 0.8797463442344267, 0.932394336758319, 0.965515026672257,
 0.8967984708313228, 0.9562847792473697, 0.9662836189055034,
 0.9187032714923455, 0.9552991998159039, 0.8721372679559742,
 0.951677098087865, 0.970701220083394, 0.880277858875798,
 0.8868837879487532, 0.8289936757848054, 0.8452643978000389,
 0.8608520989786752, 0.9408859834978103, 0.9477671884481794,
 0.9355182739828974, 0.9058402170229929, 0.888170996310456,
 0.8872799805467638, 0.872024994152445, 0.8802787599729809,
 0.9527566512472332, 0.8864763874519584, 0.8436371510886024,
 0.9828573401629994, 0.9771419297773668, 0.906019424908,
 0.9707157553507724, 0.879689193482642, 0.9436375392843368,
 0.9927180210208233, 0.9267041637380232, 0.9412299434835303,
 0.926346676233505, 0.8774254634406635, 0.8826805167518188,
 0.8865687070701256, 0.9512379465525047, 0.9641813779931143,
 0.953277273069755, 1.0047488071722177, 0.8521615788684946,
 0.8680916457728691, 0.9340561986882852, 0.9477037339014749,
 0.9469454099421577, 0.9005897924118794, 0.8803998440278067,
 0.9024692253200567, 0.909122984887152, 0.8399468552579564,
 0.9571308078096232, 0.9683939646310176, 0.9419649402214831,
 0.9613040120941247, 0.9781781986426726, 0.9805816556476108,
 0.94937687356695, 0.960693374108915, 0.9530824549428941,
 0.8843910508664925, 0.8945735422767003, 0.9049315573495563,
 0.8802084472126279, 0.8328713211676385, 0.9406572364992218,
 0.910325290850831, 0.9318781551216802, 0.8934350965988851,
 0.8353799932488288, 0.951313819820305, 0.855414485205892,
 0.909767822028357, 0.8924203614902587, 0.9408505916987862,
 0.8751269857340623, 0.938822046542, 0.9499696867836579,
 0.9605708328530759, 0.9054195520491586, 0.8859714100727238,
 0.9305256454920723, 0.937758620326129, 0.9320519159136575,
 0.9656009544636446, 0.9584255887448183, 0.8738507316066699,
 0.9661737748832995, 0.8717799481773607, 0.959731591608098,
 0.9640387155993229, 0.8600096309525227, 0.8762991916520275,
 0.9329290121054334, 0.838440295115923, 0.8399242891708862,
 0.8145405034437483, 0.961537851810333

Re: error on the diffusion tensor parameters

[Edward d'Auvergne]

Hi Vineet,

From the error message, the my_relax module is clearly a special
Python or relax module written by your former college.  It is not part
of relax, so I can't help you much.  You might be able to find it on
your system by typing:

$ locate my_relax.py
$ locate tensor_mc.py

The missing external module will have one of these names.  If it is
tensor_mc.py, then this will be in the directory my_relax/.  All the
contents of that directory is then called a Python package, and you
will need all of it.  I hope this information helps.  It is a pity
your former college did not contribute it to relax so that I can help
you more.

Regards,

Edward


On 18 December 2014 at 15:36, Panwalkar, Vineet
v.panwal...@fz-juelich.de wrote:
 Dear Edward,

 Following is the error,

 Traceback (most recent call last):
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/processor.py, 
 line 494, in run
 self.callback.init_master(self)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/__init__.py, 
 line 318, in default_init_master
 self.master.run()
   File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/relax.py, line 
 199, in run
 self.interpreter.run(self.script_file)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, 
 line 279, in run
 return run_script(intro=self.__intro_string, local=locals(), 
 script_file=script_file, show_script=self.__show_script, 
 raise_relax_error=self.__raise_relax_error)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, 
 line 585, in run_script
 return console.interact(intro, local, script_file, 
 show_script=show_script, raise_relax_error=raise_relax_error)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, 
 line 484, in interact_script
 exec_script(script_file, local)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py, 
 line 363, in exec_script
 runpy.run_module(module, globals)
   File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 180, in run_module
 fname, loader, pkg_name)
   File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 72, in _run_code
 exec code in run_globals
   File 
 /home/vpan014/NMR_900_FZJ_data/Relax/Apo_structure1_09122014/run17_structure/relax_mc_difftensor_print_all.py,
  line 11, in module
 from my_relax.tensor_mc import Main, print_fancy, Out_tensor
 ImportError: No module named my_relax.tensor_mc

 I am checking with my former labmate who wrote the script regarding the 
 module as well.

 I also had a question regarding possibility of performing Monte Carlo 
 simulations to get errors on the model free parameters within all the four 
 diffusion tensor models. I mean, normally, the MC simulations are performed 
 once a particular diffusion tensor is selected using the AIC. Is there a way 
 to do the simulations on rest of the tensor models as well?

 Cheers,

 Vineet
 

 Hi Vineet,

 Could you copy and paste the entire error?  That would significantly
 help working out what is happening, as it will indicate where the
 error is happening.  But if you search for the text my_relax or file
 my_relax.py, you will see that this has never existed in any version
 of relax, from 2001 until now.

 Regards,

 Edward

  ___

 On 18 December 2014 at 15:09, Panwalkar, Vineet
 Hi all,

 I have a script to calculate errors on the diffusion tensor parameters, 
 written by one of my former colleagues. It works well with relax v 3.2.3 
 however, in the version 3.3.3, it doesn't work and gives an error message 
 saying ImportError: No module named my_relax.tensor_mc.
 I was wondering if the module has been renamed/replaced to something else or 
 is this something entirely different.

 Thanks,

 Vineet
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 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
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 Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
 Prof. Dr. Sebastian M. Schmidt
 
 

Re: error on the diffusion tensor parameters

[Edward d'Auvergne]

Hi Vineet,

After an analysis, anything is possible using the relax user
functions.  That includes performing Monte Carlo simulations on any
model you wish.  Have a look at some of the sample scripts for the
sequence of user functions required.

Regards,

Edward



On 18 December 2014 at 16:33, Panwalkar, Vineet
v.panwal...@fz-juelich.de wrote:
 Hello Edward,

 Thanks for the reply. I am trying to get hold of all the missing modules. 
 Once they are all at one place, I will put it into relax with his permission.

 I had another small query. I was wondering if there was a possibility to 
 extract errors on the model free parameters within all the four diffusion 
 tensor models. I mean, normally, the MC simulations are performed once a 
 particular diffusion tensor is selected using the AIC. Is there a way to do 
 the this on rest of the tensor models as well, either before the AIC 
 selection or after it separately?

 Regards,

 Vineet
 
 An: Panwalkar, Vineet
 Cc: relax-users@gna.org
 Betreff: Re: error on the diffusion tensor parameters

 Hi Vineet,

 From the error message, the my_relax module is clearly a special
 Python or relax module written by your former college.  It is not part
 of relax, so I can't help you much.  You might be able to find it on
 your system by typing:

 $ locate my_relax.py
 $ locate tensor_mc.py

 The missing external module will have one of these names.  If it is
 tensor_mc.py, then this will be in the directory my_relax/.  All the
 contents of that directory is then called a Python package, and you
 will need all of it.  I hope this information helps.  It is a pity
 your former college did not contribute it to relax so that I can help
 you more.

 Regards,

 Edward


 On 18 December 2014 at 15:36, Panwalkar, Vineet
 v.panwal...@fz-juelich.de wrote:
 Dear Edward,

 Following is the error,

 Traceback (most recent call last):
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/processor.py, 
 line 494, in run
 self.callback.init_master(self)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/multi/__init__.py, 
 line 318, in default_init_master
 self.master.run()
   File /opt/scisoft64/usr/lib/python2.7/site-packages/relax/relax.py, line 
 199, in run
 self.interpreter.run(self.script_file)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py,
  line 279, in run
 return run_script(intro=self.__intro_string, local=locals(), 
 script_file=script_file, show_script=self.__show_script, 
 raise_relax_error=self.__raise_relax_error)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py,
  line 585, in run_script
 return console.interact(intro, local, script_file, 
 show_script=show_script, raise_relax_error=raise_relax_error)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py,
  line 484, in interact_script
 exec_script(script_file, local)
   File 
 /opt/scisoft64/usr/lib/python2.7/site-packages/relax/prompt/interpreter.py,
  line 363, in exec_script
 runpy.run_module(module, globals)
   File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 180, in run_module
 fname, loader, pkg_name)
   File /opt/scisoft64/usr/lib/python2.7/runpy.py, line 72, in _run_code
 exec code in run_globals
   File 
 /home/vpan014/NMR_900_FZJ_data/Relax/Apo_structure1_09122014/run17_structure/relax_mc_difftensor_print_all.py,
  line 11, in module
 from my_relax.tensor_mc import Main, print_fancy, Out_tensor
 ImportError: No module named my_relax.tensor_mc

 I am checking with my former labmate who wrote the script regarding the 
 module as well.

 I also had a question regarding possibility of performing Monte Carlo 
 simulations to get errors on the model free parameters within all the four 
 diffusion tensor models. I mean, normally, the MC simulations are performed 
 once a particular diffusion tensor is selected using the AIC. Is there a way 
 to do the simulations on rest of the tensor models as well?

 Cheers,

 Vineet
 

 Hi Vineet,

 Could you copy and paste the entire error?  That would significantly
 help working out what is happening, as it will indicate where the
 error is happening.  But if you search for the text my_relax or file
 my_relax.py, you will see that this has never existed in any version
 of relax, from 2001 until now.

 Regards,

 Edward

  ___

 On 18 December 2014 at 15:09, Panwalkar, Vineet
 Hi all,

 I have a script to calculate errors on the diffusion tensor parameters, 
 written by one of my former colleagues. It works well with relax v 3.2.3 
 however, in the version 3.3.3, it doesn't work and gives an error message 
 saying ImportError: No module named my_relax.tensor_mc.
 I was wondering if the module has been renamed/replaced to something else 
 or is this something entirely different.

 

Re: What happens if I try to do MF analysis only having 800mHz data?

[Edward d'Auvergne]

Hi Sean,

Welcome to the relax mailing lists!  I'll start by explaining how
relax can handle your single field strength data.  Firstly, I need to
point out that relax can do everything Modelfree4 does and it can
replicate the results of Modelfree4 exactly (well, almost, as real
constraint algorithms are used in relax and that used by Modelfree4
will never be added to relax).  I used this replication of Modelfree4
and Dasha behaviour as the basis for my 2008 papers
(http://dx.doi.org/10.1007/s10858-007-9214-2,
http://dx.doi.org/10.1007/s10858-007-9213-3), for understanding why
these two softwares produce sometimes quite different results.  I
don't think this was mentioned in the papers or supplement as is it so
basic in relax to do - you simply pick the same optimisation algorithm
as the other software and decrease the optimisation precision and
maximum number of optimisation iterations to match (see table 1 of the
first paper for these).

So, to perform your analysis, you need to note the difference between
the theory and optimising the model-free models verses a full analysis
protocol.  These are very different and it confuses a lot of people.
The former is fast and only takes minutes to an hour.  The later is
super-iterative and much slower, taking a day to 1-2 weeks.   There is
a lot of software out there that implements the former (Modelfree4,
Dasha, Tensor2, DYNAMICS), and then you are expected to manually take
the steps required for fulfilling the full protocol yourself (some
people don't know this and end up publishing very questionable
dynamics).  So what are the protocols?  The first full protocol was
published in the Mandel et al, 1995 paper:

http://www.nmr-relax.com/manual/The_methodology_of_Mandel_et_al_1995.html

When implemented correctly, this takes an incredible amount of time as
expensive Monte Carlo simulations are performed at each step and each
model to obtain the chi2 and F-test statistics.  As I published in my
2003 model selection paper
(http://dx.doi.org/10.1023/A:1021902006114), this should not be used.
This introduces, deliberately I should note, or the original paper
notes, bias towards the simpler models and hence less motion.  Another
major problem is the F-test.  The F-test is useful for comparing
models, but there is fine print the most people don't know about.  The
F-test is only statistically valid when the two models compared are
nested!  This is mentioned in the Numerical Recipes book series, for
example.  As The next protocol I designed based on this one and it
handles single field strength data:

http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html

It is similar in that you need and initial diffusion tensor estimate.
However it replaces the chi-squared, F-tests, and chi-squared value
empirical cut-offs with statistical AIC model selection, introduces
the concept of model elimination
(http://dx.doi.org/10.1007/s10858-006-9007-z), removes the need for
intermediate Monte Carlo simulations, and simplifies the flow of
operation.  The last protocol I'll mention here is the one I devised
to eliminate the problems associated with the initial diffusion tensor
estimate:

http://www.nmr-relax.com/manual/The_new_model_free_optimisation_protocol.html
http://www.nmr-relax.com/manual/Model_free_analysis_in_reverse.html

This is the protocol from my second 2008 paper
(http://dx.doi.org/10.1007/s10858-007-9213-3).  If you are using the
relax model-free auto-analysis (called the dauvergne_protocol, see
http://www.nmr-relax.com/api/3.3/auto_analyses.dauvergne_protocol-module.html)
or the graphical user interface (GUI), you will be using this
protocol.  I have implemented it as a fully automated auto-analysis
which is essentially just a complicated relax script.  Although this
protocol solves all of the earlier problems with model-free analyses
(protocols), it absolutely requires data at two fields.

So, how do you implement the protocol of
http://www.nmr-relax.com/manual/The_diffusion_seeded_paradigm.html for
single field strength data?  I have answered this many times on the
relax mailing lists, and it has been summarised in the following relax
wiki article:

http://wiki.nmr-relax.com/Model-free_analysis_single_field

You will find the links to the discussions there highly informative!
For the protocol described therein, most steps are present as
individual scripts in the sample_scripts/model_free/ directory.  I
have not merged these together into an automated analysis yet, mainly
due to the horrendous artefacts of using single field strength data
that are often interpreted as real dynamics.  The first step is to
obtain the initial diffusion tensor estimate.  There is no script for
this as most people use Tensor2 for this.  Neither Modelfree4 nor
Dasha implement this.  However this is not ideal as there is no clear
mapping of the spherical angles and Euler angles between Tensor2,
Modelfree4, Dasha, DYNAMICS, and relax (due to lack of documentation).
For the rest, I'll 

Re: error while running relax-GUI tutorial

[Edward d'Auvergne]

Hi Prem,

From the error message, this is within the automated analysis for
relaxation dispersion.  Creating the data pipe 'R2eff - relax_disp
(Mon Nov 17 10:50:08 2014)' can only happen once, as the 'R2eff' model
is only optimised once (there is a loop over all models).  There is
only one thing I can think of, and that is that the analysis was run
with OpenMPI.  However if the --multi='mpi4py' part of the full
command:

$ mpirun -np 8 relax --multi='mpi4py'

is missing, as:

$ mpirun -np 8 relax

Then this problem might be encountered.  Could that be what happened?
Another cause could be if the 'R2eff' model is passed into the
dispersion auto-analysis more than once in the model list though, as
you are using the GUI, this is not possible.

Cheers,

Edward




On 18 November 2014 at 22:58, Prem Raj Joseph prbj123re...@gmail.com wrote:
 Hello Edward,

 I tried the GUI version of the setup again for the relaxation dispersion
 (on the test data) and it ran without any error this time. Its possible I
 made some mistake during the setup thr last time.

 Thank again for the help

 Prem



 On Tue, Nov 18, 2014 at 5:27 AM, Edward d'Auvergne edw...@nmr-relax.com
 wrote:

 Hi Troels and Prem,

 Troels, for a suggestion for improving the script in your tutorial,
 you could use:

 
 from time import asctime, localtime

 pipe_bundle = relax_disp (%s) % asctime(localtime())
 pipe_name = origin - %s % pipe_bundle
 

 This is how the new analysis wizard in relax creates these names
 (
 http://www.nmr-relax.com/api/3.3/gui.analyses.wizard-pysrc.html#Data_pipe_page.on_display
 ).
 This script really saves a lot of time.  But, as it does not replicate
 the bug, Prem, could you still create the bug report and include all
 steps required to produce the error you observed?

 Cheers,

 Edward



 On 18 November 2014 12:08, Troels Emtekær Linnet tlin...@nmr-relax.com
 wrote:
  Hi Prem.
 
  I added the tutorial here:
 
 
 http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
 
  I tried to take power of the scripting, to get around the tedious work on
  defining the experiment settings for all spectra.
 
  So this script should take you to the end point before staring the
  analysis.
 
  Best
  Troels
 
 
 
  2014-11-18 11:51 GMT+01:00 Troels Emtekær Linnet tlin...@nmr-relax.com
 :
 
  Dear Prem.
 
  Welcome to the mailing list!
 
  I guess that you mean the manual at:
  http://www.nmr-relax.com/manual/Contents.html
 
  The relaxation dispersion auto-analysis in the GUI
 
 
 http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html
 
  Where the test data is in:
  test_suite/shared_data/dispersion/Hansen
 
  I will write it up here as a script instead.
  This goes a little faster testing.
 
  You can also find more inspiration at the wiki:
  http://wiki.nmr-relax.com
  http://wiki.nmr-relax.com/Category:Tutorials
 
  In terminal
  mkdir -p $HOME/test
  cd $HOME/test
  gedit test.py
 
  Then I build the script onwards.
  I run relax repeatedly, to execute code. Then I write new code in the
  script, and run again.
  relax test.py
 
  When I am satisfied, you can then do like this.
 
  relax -g -t log.txt
  User functions - Script - test.py
 
  THEN:
  View - Data pipe editor - Right click on pipe - Associate with a new
  Auto analysis
 
  This should bring you to a window, where all settings have been set.
 
  Relaxations dispersion models: ['R2eff', 'No Rex', 'CR72', 'NS CPMG
 2-site
  expanded']
  Grid increements: 11 (For speed-up in test phase)
  Monte-Carlo simulations number: 5 (For speed up in test phase)
 
  Then a quick click on spin.isotope function, and GO.
 
 
 
  test.py
  
  #python modules
  import os
  import glob
 
  # relax modules
  from lib.io import sort_filenames
 
  # Set path to data
  data =
 
 '/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/shared_data/dispersion/Hansen'
 
  # Create the data pipe.
  pipe_name = 'origin - relax_disp (Tue Nov 18 10:39:36 2014)'
  pipe_bundle = 'relax_disp (Tue Nov 18 10:39:36 2014)'
  pipe.create(pipe_name=pipe_name, bundle=pipe_bundle,
  pipe_type='relax_disp')
 
  # Create spin to hold data.
  sequence.read(file='fake_sequence.in', dir=data, res_num_col=1,
  res_name_col=2)
  deselect.read(file='unresolved', dir=data+os.sep+'500_MHz',
  spin_id_col=None, mol_name_col=None, res_num_col=1, boolean='AND',
  change_all=False)
  deselect.read(file='unresolved', dir=data+os.sep+'800_MHz',
  spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
  boolean='AND', change_all=False)
 
  # Give the spins attributes.
  spin.isotope(isotope='15N', spin_id='@*', force=True)
  spin.name(name='N')
 
  # Do for 800.
  ###
  # Change directory.
  os.chdir(data + os.sep + '500_MHz')
 
  # Get the file list, and sort the file list Alphanumeric.
  flist500 = glob.glob('*.in_sparky')
  flist500 = sort_filenames(filenames=flist500)
 
  # Make

Re: error while running relax-GUI tutorial

[Edward d'Auvergne]

Hi Troels,

For the tutorial at
http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI
, I would suggest also adding that relax can be run using OpenMPI to
speed up the relaxation dispersion analysis.  So that if you have a
machine with 8 cores and OpenMPI and python-mpi4py installed
(http://www.nmr-relax.com/manual/The_multi_processor_framework.html),
you can run relax with 7 slaves by typing:

$ mpirun -n 8 relax --multi='mpi4py' --gui --tee my.log

Regards,

Edward



On 18 November 2014 12:27, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Hi Troels and Prem,

 Troels, for a suggestion for improving the script in your tutorial,
 you could use:

 
 from time import asctime, localtime

 pipe_bundle = relax_disp (%s) % asctime(localtime())
 pipe_name = origin - %s % pipe_bundle
 

 This is how the new analysis wizard in relax creates these names
 (http://www.nmr-relax.com/api/3.3/gui.analyses.wizard-pysrc.html#Data_pipe_page.on_display).
 This script really saves a lot of time.  But, as it does not replicate
 the bug, Prem, could you still create the bug report and include all
 steps required to produce the error you observed?

 Cheers,

 Edward



 On 18 November 2014 12:08, Troels Emtekær Linnet tlin...@nmr-relax.com 
 wrote:
 Hi Prem.

 I added the tutorial here:

 http://wiki.nmr-relax.com/Tutorial_for_The_relaxation_dispersion_auto-analysis_in_the_GUI

 I tried to take power of the scripting, to get around the tedious work on
 defining the experiment settings for all spectra.

 So this script should take you to the end point before staring the
 analysis.

 Best
 Troels



 2014-11-18 11:51 GMT+01:00 Troels Emtekær Linnet tlin...@nmr-relax.com:

 Dear Prem.

 Welcome to the mailing list!

 I guess that you mean the manual at:
 http://www.nmr-relax.com/manual/Contents.html

 The relaxation dispersion auto-analysis in the GUI

 http://www.nmr-relax.com/manual/The_relaxation_dispersion_auto_analysis_in_the_GUI.html

 Where the test data is in:
 test_suite/shared_data/dispersion/Hansen

 I will write it up here as a script instead.
 This goes a little faster testing.

 You can also find more inspiration at the wiki:
 http://wiki.nmr-relax.com
 http://wiki.nmr-relax.com/Category:Tutorials

 In terminal
 mkdir -p $HOME/test
 cd $HOME/test
 gedit test.py

 Then I build the script onwards.
 I run relax repeatedly, to execute code. Then I write new code in the
 script, and run again.
 relax test.py

 When I am satisfied, you can then do like this.

 relax -g -t log.txt
 User functions - Script - test.py

 THEN:
 View - Data pipe editor - Right click on pipe - Associate with a new
 Auto analysis

 This should bring you to a window, where all settings have been set.

 Relaxations dispersion models: ['R2eff', 'No Rex', 'CR72', 'NS CPMG 2-site
 expanded']
 Grid increements: 11 (For speed-up in test phase)
 Monte-Carlo simulations number: 5 (For speed up in test phase)

 Then a quick click on spin.isotope function, and GO.



 test.py
 
 #python modules
 import os
 import glob

 # relax modules
 from lib.io import sort_filenames

 # Set path to data
 data =
 '/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/test_suite/shared_data/dispersion/Hansen'

 # Create the data pipe.
 pipe_name = 'origin - relax_disp (Tue Nov 18 10:39:36 2014)'
 pipe_bundle = 'relax_disp (Tue Nov 18 10:39:36 2014)'
 pipe.create(pipe_name=pipe_name, bundle=pipe_bundle,
 pipe_type='relax_disp')

 # Create spin to hold data.
 sequence.read(file='fake_sequence.in', dir=data, res_num_col=1,
 res_name_col=2)
 deselect.read(file='unresolved', dir=data+os.sep+'500_MHz',
 spin_id_col=None, mol_name_col=None, res_num_col=1, boolean='AND',
 change_all=False)
 deselect.read(file='unresolved', dir=data+os.sep+'800_MHz',
 spin_id_col=None, mol_name_col=None, res_num_col=1, res_name_col=2,
 boolean='AND', change_all=False)

 # Give the spins attributes.
 spin.isotope(isotope='15N', spin_id='@*', force=True)
 spin.name(name='N')

 # Do for 800.
 ###
 # Change directory.
 os.chdir(data + os.sep + '500_MHz')

 # Get the file list, and sort the file list Alphanumeric.
 flist500 = glob.glob('*.in_sparky')
 flist500 = sort_filenames(filenames=flist500)

 # Make ID
 ID500 = []
 for f in flist500: ID500.append(500_+f.split(.in_sparky)[0])

 # Then Read
 spectrum.read_intensities(file=flist500, spectrum_id=ID500)

 # Repeat for the replicated spectra.
 flist500rep = glob.glob('*in.bis_sparky')
 flist500rep = sort_filenames(filenames=flist500rep)

 # Make ID
 ID500rep = []
 for f in flist500rep:
 ID500rep.append(500_+f.split(.in.bis_sparky)[0]+'b')

 # Then Read
 spectrum.read_intensities(file=flist500rep, spectrum_id=ID500rep)

 # Then map replicated
 for b_id in ID500rep:
 a_id = b_id[:-1]
 spectrum.replicated(spectrum_ids=[a_id, b_id])

 # Then check
 print cdp.replicates

 # Then repeat for 800.
 ###
 # Change

Re: C modules not compiled

[Edward d'Auvergne]

Hi Mark,

Welcome to the relax mailing lists!  The problem you see could be due
to a number of factors.  Firstly, could you check if you have the
compiled file present on your system:

$ ls -alh /usr/local/relax/target_functions/relax_fit.so
$ file /usr/local/relax/target_functions/relax_fit.so


If the file is there, then maybe you have a Python version problem.
The C module was compiled using Python 2.7.  Normally this will then
work for Python 2.5, 2.6 and 2.7 but not Python = 3.1 (I have a Linux
set up, both 32 and 64-bit with all versions of Python from 1.0 to 3.4
that I regularly check this with).  You can check this by running
relax and typing:

relax import target_functions.relax_fit


For example in Python 3, this gives the error:

relax import target_functions.relax_fit
Traceback (most recent call last):
  File console, line 1, in module
ImportError: /data/relax/relax-trunk/target_functions/relax_fit.so:
undefined symbol: Py_InitModule4_64


Maybe you will see something similar.  In any case you have two
alternatives.  The first is to upgrade Python, if the relax_fit.so
file exists, though this can be a painful and dangerous task on Linux
systems (you can change the base 'relax' file to point to a different
alternative Python version if you wish).  The second is as Troels
suggests.  Install the scons program, the Python headers, and then
just run 'scons' as root in the /usr/local/relax directory to compile
the module yourself.

Note that you only need this C module for fitting exponential curves
for the R1, R2, or relaxation dispersion analyses.

Regards,

Edward





On 14 November 2014 01:05, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Hi.

 Try just write scons

 But this should only be for the source code.

 The packaged versions should already have the compiled C code in it.

 So this is weird.

 Can you run
 relax - d
 and post it here?

 Best
 Troels
 On 13 Nov 2014 22:34, Maciejewski,Mark W. ma...@uchc.edu wrote:

 Hello,

 I have installed relax 3.2.3 on CentOS release 6.6. The program runs fine
 except for the error:
 ImportError: relaxation curve fitting is unavailable, the corresponding C
 modules have not been compiled.

 I installed relax using the command:
 scons install

 I have searched the archives and see that others have had similar
 problems, but cannot find a solution that works for me.

 Any suggestions on how to install or compile the C modules?

 Below is the output from relax -info

 Thanks,
 Mark


 [nmradmin@nmrbox_wisc ~]$ relax --info



 relax 3.2.3

   Molecular dynamics by NMR data analysis

  Copyright (C) 2001-2006 Edward d'Auvergne
  Copyright (C) 2006-2014 the relax development team

 This is free software which you are welcome to modify and redistribute
 under the conditions of the
 GNU General Public License (GPL).  This program, including all modules, is
 licensed under the GPL
 and comes with absolutely no warranty.  For details type 'GPL' within the
 relax prompt.

 Assistance in using the relax prompt and scripting interface can be
 accessed by typing 'help' within
 the prompt.

 ImportError: relaxation curve fitting is unavailable, the corresponding C
 modules have not been compiled.

 Processor fabric:  Uni-processor.


 Hardware information:
 Machine: x86_64
 Processor:   x86_64
 Processor name:  Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
 Endianness:  little
 Total RAM size:  3832 Mb
 Total swap size: 3967 Mb

 Operating system information:
 System:  Linux
 Release: 2.6.32-504.1.3.el6.x86_64
 Version: #1 SMP Tue Nov 11 17:57:25 UTC 2014
 GNU/Linux version:   CentOS 6.6 Final
 Distribution:centos 6.6 Final
 Full platform string:
 Linux-2.6.32-504.1.3.el6.x86_64-x86_64-with-centos-6.6-Final

 Python information:
 Architecture:64bit ELF
 Python version:  2.6.6
 Python branch:   tags/r266
 Python build:r266:84292, Jan 22 2014 09:42:36
 Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-4)
 Libc version:glibc 2.2.5
 Python implementation:   CPython
 Python revision: 84292
 Python executable:   /usr/bin/python
 Python flags:sys.flags(debug=0, py3k_warning=0,
 division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0,
 dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
 tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
 Python float info:   sys.floatinfo(max=1.7976931348623157e+308,
 max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
 min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.2204460492503131e-16,
 radix=2, rounds=1)
 Python module path

Re: C modules not compiled

[Edward d'Auvergne]

Hi Mark,

I would also recommend that you sign up for the relax-announce mailing
list (https://mail.gna.org/listinfo/relax-announce/).  This list only
receives a few emails per year (see
http://news.gmane.org/gmane.science.nmr.relax.announce), and it is
used almost exclusively for announcing new relax versions, for example
relax 3.3.2 which I am in the process of releasing now (see
http://www.nmr-relax.com/download.html).  Since relax 3.2.3, there
have been the following releases:

http://wiki.nmr-relax.com/Relax_3.3.0
http://wiki.nmr-relax.com/Relax_3.3.1
http://wiki.nmr-relax.com/Relax_3.3.2

That last link will appear later today.  If you are performing either
a model-free or relaxation dispersion analysis, I would highly
recommend that you upgrade to relax 3.3.2 to obtain all the bug fixes
and Troels' huge relaxation dispersion speed ups
(http://wiki.nmr-relax.com/Relax_3.3.0).

Regards,

Edward


On 14 November 2014 10:19, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Hi Mark,

 Welcome to the relax mailing lists!  The problem you see could be due
 to a number of factors.  Firstly, could you check if you have the
 compiled file present on your system:

 $ ls -alh /usr/local/relax/target_functions/relax_fit.so
 $ file /usr/local/relax/target_functions/relax_fit.so


 If the file is there, then maybe you have a Python version problem.
 The C module was compiled using Python 2.7.  Normally this will then
 work for Python 2.5, 2.6 and 2.7 but not Python = 3.1 (I have a Linux
 set up, both 32 and 64-bit with all versions of Python from 1.0 to 3.4
 that I regularly check this with).  You can check this by running
 relax and typing:

 relax import target_functions.relax_fit


 For example in Python 3, this gives the error:

 relax import target_functions.relax_fit
 Traceback (most recent call last):
   File console, line 1, in module
 ImportError: /data/relax/relax-trunk/target_functions/relax_fit.so:
 undefined symbol: Py_InitModule4_64


 Maybe you will see something similar.  In any case you have two
 alternatives.  The first is to upgrade Python, if the relax_fit.so
 file exists, though this can be a painful and dangerous task on Linux
 systems (you can change the base 'relax' file to point to a different
 alternative Python version if you wish).  The second is as Troels
 suggests.  Install the scons program, the Python headers, and then
 just run 'scons' as root in the /usr/local/relax directory to compile
 the module yourself.

 Note that you only need this C module for fitting exponential curves
 for the R1, R2, or relaxation dispersion analyses.

 Regards,

 Edward





 On 14 November 2014 01:05, Troels Emtekær Linnet tlin...@gmail.com wrote:
 Hi.

 Try just write scons

 But this should only be for the source code.

 The packaged versions should already have the compiled C code in it.

 So this is weird.

 Can you run
 relax - d
 and post it here?

 Best
 Troels
 On 13 Nov 2014 22:34, Maciejewski,Mark W. ma...@uchc.edu wrote:

 Hello,

 I have installed relax 3.2.3 on CentOS release 6.6. The program runs fine
 except for the error:
 ImportError: relaxation curve fitting is unavailable, the corresponding C
 modules have not been compiled.

 I installed relax using the command:
 scons install

 I have searched the archives and see that others have had similar
 problems, but cannot find a solution that works for me.

 Any suggestions on how to install or compile the C modules?

 Below is the output from relax -info

 Thanks,
 Mark


 [nmradmin@nmrbox_wisc ~]$ relax --info



 relax 3.2.3

   Molecular dynamics by NMR data analysis

  Copyright (C) 2001-2006 Edward d'Auvergne
  Copyright (C) 2006-2014 the relax development team

 This is free software which you are welcome to modify and redistribute
 under the conditions of the
 GNU General Public License (GPL).  This program, including all modules, is
 licensed under the GPL
 and comes with absolutely no warranty.  For details type 'GPL' within the
 relax prompt.

 Assistance in using the relax prompt and scripting interface can be
 accessed by typing 'help' within
 the prompt.

 ImportError: relaxation curve fitting is unavailable, the corresponding C
 modules have not been compiled.

 Processor fabric:  Uni-processor.


 Hardware information:
 Machine: x86_64
 Processor:   x86_64
 Processor name:  Intel(R) Xeon(R) CPU E5-1620 0 @ 3.60GHz
 Endianness:  little
 Total RAM size:  3832 Mb
 Total swap size: 3967 Mb

 Operating system information:
 System:  Linux
 Release: 2.6.32-504.1.3.el6.x86_64
 Version: #1 SMP Tue Nov 11 17:57:25 UTC 2014
 GNU/Linux version:   CentOS 6.6 Final
 Distribution:centos 6.6 Final
 Full platform string:
 Linux-2.6.32-504.1.3.el6

Re: Reg : Input files for model free analysis

[Edward d'Auvergne]

Dear Srinivasa,

If you search the BMRB database, there is a lot of published
relaxation data (and model-free results) deposited there.  This type
of data is not distributed with relax, as the BMRB is the correct
place to deposit data, and the relax bmrb.read user function will read
all the data out of the BMRB files.

However if you really need, you might be able to use data in the
directories such as
test_suite/shared_data/diffusion_tensor/ellipsoid/.  You could load
the relaxation data and use the uniform.pdb structure.  But I don't
know how far you will get.  If you are worried about using relax, just
run the graphical user interface (GUI) by running relax as:

$ relax --gui

If you use the tutorial in the relax manual
(http://www.nmr-relax.com/manual/new_protocol_in_GUI.html), but using
your own data, it should be very simple to complete an analysis.

Regards,

Edward



On 10 October 2014 23:29, srinivas penumutchu
penumutchu.srini...@gmail.com wrote:
 Dear Relax users,

 I am new to use Relax software , I want input files of model free analysis
 to practice on Relax software , it would be great help to me if you can
 input files to use the relax ?

 Thanking you for great help

 --


 *Best Regards *







 *Srinivasa Rao PenumutchuResearch Scholar Protein NMR Lab , II floor-218
 Department of Chemistry National Tsing Hua University, Hsinchu, Taiwan. Ph:
 886357151-35605,M:+886-912894534 ,   *

 *  Email- penumutchu.srini...@gmail.com penumutchu.srini...@gmail.com *
 ___
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 relax-users@gna.org

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 https://mail.gna.org/listinfo/relax-users

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Re: Regarding Relax-3.3.0 NMR installation

[Edward d'Auvergne]

Dear Arun,

Welcome to the relax mailing lists.  The unzipping to the C:\program
files problem you see is not relax specific.  This can sometimes
happen due to Windows security settings.  A quick internet search will
show innumerable instances of Windows users with the same issue.

As for the GUI, how to you run it?  Do you run relax using:

$ relax --gui

It could be that wxPython is not set up correctly.  Could you run the command:

$ relax -i --tee relax_info.log

This will output a lot of information about your setup and might
indicate what the problem is.  It will also create the relax_info.log
file which is easier for Windows uses to copy the text from.  Could
you copy and paste the contents of that into an email?  Please do not
attach a file to the mailing list message - this will be automatically
stripped out of the message so it will not be seen.  A good test that
wxPython is working is to also download the demo files
(http://www.wxpython.org/download.php#msw).  These must be of the same
version as your wxPython installation.  If you cannot run the demo,
then the problem is with wxPython and not relax.  I hope this helps.

Regards,

Edward


P. S.  Sorry for the late reply.  My email system thought your email
was spam, so I didn't see it until today.


On 8 September 2014 23:32, Arun Gupta arungupta...@yahoo.com wrote:


 Hi

 I have tried to  install Relax NMR software on my
 Windows 8 O.S with Python2.7.8 . However when I try to unzip the relax-3.3.0
 zipped folder to program files. I get message access denied although I am 
 trying
 to install administrator settings. However  the zip file can be  unzipped in
 other folder and copied to C:/ folder but the relax-3.3.0 GUI interface 
 doesn't
  come on model_free. command. Can you suggest solution to these
 issues

 Regards

 Arun
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 relax-users@gna.org

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 reminder, or change your subscription options,
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 https://mail.gna.org/listinfo/relax-users

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Re: How does the error intensity analysis handle both specification of baseplane RMSD and partly repeated spectrum?

[Edward d'Auvergne]

Hi Troels,

Currently you can only choose one technique or the other.  You will
see this in the algorithm for choosing between the different
techniques in the pipe_control.spectrum.error_analysis() function
(http://www.nmr-relax.com/api/3.3/pipe_control.spectrum-pysrc.html#error_analysis).
Replicates come first, if present, and that will be used for error.
This calls __errors_repl().  If no replicates exist, then either
__errors_height_no_repl() or __errors_vol_no_repl() are called.
Coming up with an algorithm that does a mixture of both will be
difficult.  And it will also be complicated to explain the behaviour
to the user, though that is currently done using printouts.

Regards,

Edward

On 12 September 2014 14:22, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Dear Edward.

 I was wondering how relax handles the error intensity analysis,
 where one both specify the baseplane RMSD and and one also have partly
 repeated spectrums?


 For example you have recorded for 10 time series.

 You measure the baseplane RMSD for each spectrum.

 You have repeated spectrum 1,2 and 7,8.

 You specify all this to relax.

 Best
 Troels

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 relax-users@gna.org

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 reminder, or change your subscription options,
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 https://mail.gna.org/listinfo/relax-users

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Re: Relaxation dispersion clustering calculation time

[Edward d'Auvergne]

Hi Chung-ke,

The aim of relax is to support absolutely every NMR dynamics theory in
existence!  For the relaxation dispersion analysis section of relax,
this means supporting all published models for the dispersion data,
and all parametric restrictions of these models.  Many of the
dispersion models have been derived with the assumption that R20A and
R20B are different, the Carver and Richards model is a good example of
this (http://wiki.nmr-relax.com/CR72_full).  These are the '* full'
models in relax.  However in the literature the parametric restriction
R20A = R20B (= R20) is almost always used.  For the analytic models
this can significantly simplify the equations, whereas for the numeric
models the equations do not change.  In both cases, two dimensions of
the the optimisation space collapse into one and the optimisation
problem massively simplifies.  That is why in relax we also provide
the collapsed models (those with the ' full' part of the label
removed).

It is true most literature data is not suitable for the '* full'
models.  That is why they are not turned on by default in the GUI or
listed in the sample scripts.  From memory though, there are cases
whereby the measured data is of high enough quality and collected on
enough magnets that the R20A != R20B assumption can be made.  I cannot
remember the reference(s), but it shouldn't be too hard to find.
Anyway, the full R20A != R20B models are provided in relax for a
number of reasons:

  - The rare cases whereby the data is good enough.
  - Academic studies.
  - Future developments could significantly improve the quality of
measured dispersion data so that the R20A != R20B assumption can be
regularly made.
  - Chemists have a different perspective on life compared to
biologists.  Small organic molecules make the R20A vs. R20B
distinction much, much easier.

I hope it is now clearer why there are these models in relax.

Regards,

Edward




On 10 September 2014 15:27, Chung-ke Chang chun...@ibms.sinica.edu.tw wrote:
 Dear Edward and Troels,

 Thank you all for the help! We are currently testing the new version of relax 
 (yes, we are using the “normal” release), and making sure it plays along 
 nicely with other software - we have a plethora of different python versions, 
 which the system manager is doing his best to avoid interfering with each 
 other. I am curious about one thing though: If the ‘CR72 full’ model has not 
 been used in any published studies, then is there any reason to include it 
 when trying to fit “real-world” data? It seems that Troels is implying that 
 “real-world” data is too noisy to obtain meaningful fitting parameters from 
 the model. Or am I misunderstanding something?

 Cheers,

 Chung-ke

 On Sep 9, 2014, at 8:56 PM, Edward d'Auvergne edw...@nmr-relax.com wrote:

 Hi Chung-ke,

 The only way to find out about new relax releases is the
 relax-announce mailing list
 (http://news.gmane.org/gmane.science.nmr.relax.announce).  Some relax
 users were signed up for the freecode announcements
 (http://freecode.com/projects/nmr-relax), but freecode has
 unfortunately shut down (http://freecode.com/about).

 For the version you are currently using, note that this is the
 repository version of relax installed by the superuser.  You should
 make sure you use the normal releases, as the repository version can
 sometimes be in a broken or buggy state as development occurs.  You
 can also have a copy in your home directory by typing:

 $ svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk
 $ cd relax-trunk
 $ scons

 If you already have a repository version on your system, these
 commands should just work.  But you should only use the repository
 version if you would like a bug fix and cannot wait until the next
 relax release.

 Regards,

 Edward



 On 9 September 2014 10:37, Chung-ke Chang chun...@ibms.sinica.edu.tw wrote:
 Dear Troels and Edward,

 Thank you for the pointers. I was not aware that a new version was out last
 week, so I’ve asked the IT people to install it on our cluster. Below is the
 output from ‘relax -i’:

 [chungke@nmrc10 onc_dAUGA_MES_310K]$ relax -i



  relax repository checkout r24533
 svn://svn.gna.org/svn/relax/trunk

  Molecular dynamics by NMR data analysis

 Copyright (C) 2001-2006 Edward d'Auvergne
 Copyright (C) 2006-2014 the relax development team

 This is free software which you are welcome to modify and redistribute under
 the conditions of the
 GNU General Public License (GPL).  This program, including all modules, is
 licensed under the GPL
 and comes with absolutely no warranty.  For details type 'GPL' within the
 relax prompt.

 Assistance in using the relax prompt and scripting interface can be accessed
 by typing 'help' within
 the prompt.

 Processor fabric:  Uni-processor.


 Hardware information:
Machine: x86_64

Re: Relaxation dispersion clustering calculation time

[Edward d'Auvergne]

Hi Chung-ke,

The only way to find out about new relax releases is the
relax-announce mailing list
(http://news.gmane.org/gmane.science.nmr.relax.announce).  Some relax
users were signed up for the freecode announcements
(http://freecode.com/projects/nmr-relax), but freecode has
unfortunately shut down (http://freecode.com/about).

For the version you are currently using, note that this is the
repository version of relax installed by the superuser.  You should
make sure you use the normal releases, as the repository version can
sometimes be in a broken or buggy state as development occurs.  You
can also have a copy in your home directory by typing:

$ svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk
$ cd relax-trunk
$ scons

If you already have a repository version on your system, these
commands should just work.  But you should only use the repository
version if you would like a bug fix and cannot wait until the next
relax release.

Regards,

Edward



On 9 September 2014 10:37, Chung-ke Chang chun...@ibms.sinica.edu.tw wrote:
 Dear Troels and Edward,

 Thank you for the pointers. I was not aware that a new version was out last
 week, so I’ve asked the IT people to install it on our cluster. Below is the
 output from ‘relax -i’:

 [chungke@nmrc10 onc_dAUGA_MES_310K]$ relax -i



   relax repository checkout r24533
  svn://svn.gna.org/svn/relax/trunk

   Molecular dynamics by NMR data analysis

  Copyright (C) 2001-2006 Edward d'Auvergne
  Copyright (C) 2006-2014 the relax development team

 This is free software which you are welcome to modify and redistribute under
 the conditions of the
 GNU General Public License (GPL).  This program, including all modules, is
 licensed under the GPL
 and comes with absolutely no warranty.  For details type 'GPL' within the
 relax prompt.

 Assistance in using the relax prompt and scripting interface can be accessed
 by typing 'help' within
 the prompt.

 Processor fabric:  Uni-processor.


 Hardware information:
 Machine: x86_64
 Processor:   x86_64
 Processor name:  Intel(R) Xeon(R) CPU   E5430  @ 2.66GHz
 Endianness:  little
 Total RAM size:  7983 Mb
 Total swap size: 8189 Mb

 Operating system information:
 System:  Linux
 Release: 2.6.18-164.el5
 Version: #1 SMP Thu Sep 3 03:28:30 EDT 2009
 Distribution:redhat 5.3 Final
 Full platform string:
 Linux-2.6.18-164.el5-x86_64-with-redhat-5.3-Final

 Python information:
 Architecture:64bit ELF
 Python version:  2.5.1
 Python build:r251:54863, Jul 23 2008 17:35:20
 Python compiler: GCC Intel(R) C++ gcc 4.1 mode
 Libc version:glibc 2.3
 Python executable:   /program/nmr/bin/python
 Python module path:  ['/program/nmr/relax',
 '/program/nmr/lib/python2.5/site-packages/setuptools-0.6c9-py2.5.egg',
 '/program/nmr/lib/python25.zip', '/program/nmr/lib/python2.5',
 '/program/nmr/lib/python2.5/plat-linux2',
 '/program/nmr/lib/python2.5/lib-tk',
 '/program/nmr/lib/python2.5/lib-dynload',
 '/program/nmr/lib/python2.5/site-packages',
 '/program/nmr/lib/python2.5/site-packages/Scientific/linux2']

 Python packages and modules (most are optional):

 Name   InstalledVersion Path
 minfx  True 1.0.8
 /program/nmr/lib/python2.5/site-packages/minfx
 bmrblibTrue 1.0.3
 /program/nmr/lib/python2.5/site-packages/bmrblib
 numpy  True 1.6.2
 /program/nmr/lib/python2.5/site-packages/numpy
 scipy  False
 wxPython   False
 matplotlib True 0.98.3
 /program/nmr/lib/python2.5/site-packages/matplotlib
 mpi4py True 1.3.1
 /program/nmr/lib/python2.5/mpi4py
 epydoc False
 optparse   True 1.5.3
 /program/nmr/lib/python2.5/optparse.pyc
 readline   True
 /program/nmr/lib/python2.5/lib-dynload/readline.so
 profileTrue
 /program/nmr/lib/python2.5/profile.pyc
 bz2True
 /program/nmr/lib/python2.5/lib-dynload/bz2.so
 gzip   True
 /program/nmr/lib/python2.5/gzip.pyc
 io False
 xmlTrue 0.8.4 (internal)
 /program/nmr/lib/python2.5/xml/__init__.pyc
 xml.dom.minidomTrue
 /program/nmr/lib/python2.5/xml/dom/minidom.pyc

 relax information:
 Version: repository checkout r24533
 svn://svn.gna.org/svn/relax/trunk
 Processor fabric:Uni-processor.

 relax C modules:

 ModuleCompiledFile type
 Path
 target_functions.relax_fitTrueELF 64-bit LSB shared object, AMD
 x86-64, version 1 (SYSV), not stripped
 /program/nmr/relax/target_functions

Re: Is there a way to clear the Monte Carlo simulation data key?

[Edward d'Auvergne]

Hi,

Could you describe a situation that covers this?  What do you mean by
the Monte Carlo simulation data key?  In the data pipe and spin
containers, the Monte Carlo simulation optimisation results are
usually stored in the *_sim data structures as lists, and the errors
from the simulations in the *_err data structures which are simple
floats.  But this is dependent on the analysis and data type - some
model parameters can be single values, lists of values, or
dictionaries of values, and this is preserved in the Monte Carlo
simulation structures as well.

Regards,

Edward


On 28 August 2014 11:14, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Dear Edward.

 Is there a way to clear the Monte Carlo simulation data key?

 I try to run some data with increasing number of Monte Carlo simulations.

 Thank you.
 Best
 Troels

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Re: Is there a way to clear the Monte Carlo simulation data key?

[Edward d'Auvergne]

Hi,

Maybe you should consider adding this to the monte_carlo.setup user
function?  Is the problem that you cannot run Monte Carlo simulations
twice with a different number of simulations?  This should really be
handled by monte_carlo.setup.

Regards,

Edward



On 28 August 2014 11:25, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Allright, I found a fix.


 # Make Carlo Simulations number
 mc_number_list = range(5, 100, 20)

 sim_attr_list = ['chi2_sim', 'f_count_sim', 'g_count_sim',
 'h_count_sim', 'i0_sim', 'iter_sim', 'peak_intensity_sim',
 'r2eff_sim', 'select_sim', 'warning_sim']

 # Loop over the Monte Carlo simulations:
 for number in mc_number_list:
 # First delete old simulations.
 for cur_spin, mol_name, resi, resn, spin_id in
 spin_loop(full_info=True, return_id=True, skip_desel=True):
 # Loop over the simulated attributes.
 for sim_attr in sim_attr_list:
 if hasattr(cur_spin, sim_attr):
 delattr(cur_spin, sim_attr)

 self.interpreter.monte_carlo.setup(number=number)
 self.interpreter.monte_carlo.create_data()
 self.interpreter.monte_carlo.initial_values()
 self.interpreter.minimise.execute(min_algor=min_algor,
 constraints=constraints)
 self.interpreter.eliminate()
 self.interpreter.monte_carlo.error_analysis()

 est_key = 'mc_%s'%number
 est_keys.append(est_key)

 # Collect data.
 for cur_spin, mol_name, resi, resn, spin_id in
 spin_loop(full_info=True, return_id=True, skip_desel=True):
 # Add key for estimate.
 my_dic[spin_id][est_key] = {}

 for exp_type, frq, offset, point, ei, mi, oi, di in
 loop_exp_frq_offset_point(return_indices=True):
 # Generate the param_key.
 param_key = return_param_key_from_data(exp_type=exp_type,
 frq=frq, offset=offset, point=point)

 # Add key to dic.
 my_dic[spin_id][est_key][param_key] = {}

 # Get the value.
 r2eff = getattr(cur_spin, 'r2eff')[param_key]
 r2eff_err = getattr(cur_spin, 'r2eff_err')[param_key]
 i0 = getattr(cur_spin, 'i0')[param_key]
 i0_err = getattr(cur_spin, 'i0_err')[param_key]

 # Save to dic.
 my_dic[spin_id][est_key][param_key]['r2eff'] = r2eff
 my_dic[spin_id][est_key][param_key]['r2eff_err'] = r2eff_err
 my_dic[spin_id][est_key][param_key]['i0'] = i0
 my_dic[spin_id][est_key][param_key]['i0_err'] = i0_err

 2014-08-28 11:20 GMT+02:00 Edward d'Auvergne edw...@nmr-relax.com:
 Hi,

 Could you describe a situation that covers this?  What do you mean by
 the Monte Carlo simulation data key?  In the data pipe and spin
 containers, the Monte Carlo simulation optimisation results are
 usually stored in the *_sim data structures as lists, and the errors
 from the simulations in the *_err data structures which are simple
 floats.  But this is dependent on the analysis and data type - some
 model parameters can be single values, lists of values, or
 dictionaries of values, and this is preserved in the Monte Carlo
 simulation structures as well.

 Regards,

 Edward


 On 28 August 2014 11:14, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Dear Edward.

 Is there a way to clear the Monte Carlo simulation data key?

 I try to run some data with increasing number of Monte Carlo simulations.

 Thank you.
 Best
 Troels

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Re: field strength off-resonance R1rho constant relax time relaxation dispersion

[Edward d'Auvergne]

Hi Atul,

As Troels asked, could you create a support request with the link
https://gna.org/support/?func=additemgroup=relax and attach the files
there?  Files should not be attached to public mailing list messages
as it puts a large amount of strain on the infrastructure, not only
with the mail server but also the 4 independent mailing list archives:

https://mail.gna.org/public/relax-users/2014-08/msg00025.html
http://www.mail-archive.com/relax-users@gna.org/msg01672.html
http://thread.gmane.org/gmane.science.nmr.relax.user/1735/focus=1736
http://marc.info/?l=relax-usersr=1w=2

As you can see from these archived messages, your attachment has been
stripped out of your email.  The relax mail server is configured to
delete all attachments before sending out the message.

For your problem, I think I might now understand the issue.  But it
would still be useful to have the files attached to the support
request for future reference.  If you would like to keep the data
private, then maybe delete all data in the files except for one or two
residues (this also helps for converting the data into a relax system
test).  And you could also slightly randomise the peak intensity
values if you really want to keep the real data private.

The issue is that the ordering of relaxation dispersion data in relax
is as follows:

1)  Experiment type (certain dispersion models handle mixed experiment
types, for example the MMQ models,
2)  The spins of the cluster,
3)  Magnetic field strength,
4)  Offsets (for both R1rho and CPMG, though off-resonance CPMG models
such as in CATIA are yet to be added to relax),
5)  Dispersion points (nu_CPMG and nu_1).

So for 5), you only have one point per offset.  But to specify the
reference, this needs to be at the lower dispersion point level.  So
for each offset value, you will need to have your reference and the
point.  You need to make relax load the reference peak intensities
multiple times, once for each offset value.  So maybe you need:

-
data = [
['900MHz_reference','ref_off_reso_R1rho_ubi_1.list',   2100,
None, 0.320,  900.0e6, 9],
['900MHz_2100','2100_off_reso_R1rho_ubi_2.list',   2100,
1500, 0.320,  900.0e6, 9],
['900MHz_reference','ref_off_reso_R1rho_ubi_1.list',   2728,
None, 0.320,  900.0e6, 9],
['900MHz_2728','2728_off_reso_R1rho_ubi_3.list',   2728,
1500, 0.320,  900.0e6, 9],
['900MHz_reference','ref_off_reso_R1rho_ubi_1.list',   3357,
None, 0.320,  900.0e6, 9],
['900MHz_3357','3357_reso_R1rho_ubi_4.list',   3357,
1500, 0.320,  900.0e6, 9],
['900MHz_reference','ref_off_reso_R1rho_ubi_1.list',   3985,
None, 0.320,  900.0e6, 9],
['900MHz_3985','3985_off_reso_R1rho_ubi_5.list',   3985,
1500, 0.320,  900.0e6, 9],
['900MHz_reference','ref_off_reso_R1rho_ubi_1.list',   4614,
None, 0.320,  900.0e6, 9],
['900MHz_4614','4614_off_reso_R1rho_ubi_6.list',   4614,
1500, 0.320,  900.0e6, 9],
['900MHz_rep_4614','4614_rep_off_reso_R1rho_ubi_10.list',  4614,
1500, 0.320,  900.0e6, 9],
['900MHz_reference','ref_off_reso_R1rho_ubi_1.list',   5242,
None, 0.320,  900.0e6, 9],
['900MHz_5242','5242_off_reso_R1rho_ubi_7.list',   5242,
1500, 0.320,  900.0e6, 9],
['900MHz_reference','ref_off_reso_R1rho_ubi_1.list',   5871,
None, 0.320,  900.0e6, 9],
['900MHz_5871','5871_off_reso_R1rho_ubi_8.list',   5871,
1500, 0.320,  900.0e6, 9],
['900MHz_reference','ref_off_reso_R1rho_ubi_1.list',   6500,
None, 0.320,  900.0e6, 9],
['900MHz_6500','6500_off_reso_R1rho_ubi_9.list',   6500,
1500, 0.320,  900.0e6, 9]
]
---

Please carefully check the printouts to make sure the correct numbers
are being sent into the correct user functions.  Specifying the
reference at the higher offset level is not yet supported in relax.
But with your data set attached to a support request, maybe in the
future it could be turned into a relax system test and such a feature
implemented.  I hope this information helps.

Regards,

Edward


On 22 August 2014 23:01, Atul Srivastava asriv...@umn.edu wrote:
 Dear Edward,

 Thanks for providing help and insights. I used an improved script. The
 scripts is able to calculate the R2eff and the omegaeffective properly, but
 it is not able to fit any model. It also sees dispersion point as a constant
 1500 Hz (see attached file in results/R2eff/disp_55_N.out).

 I have attached all sample data, script and results for your review. Please
 see the last few lines in the log file for the error message.

 Thanks,
 Atul




 On Fri, Aug 22, 2014 at 3:02 AM, Edward

Re: field strength off-resonance R1rho constant relax time relaxation dispersion

[Edward d'Auvergne]

Hi Atul,

Continuing from Troels' post at
http://thread.gmane.org/gmane.science.nmr.relax.user/1718/focus=1732,
this time with the ppm units:


On 21 August 2014 12:00, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Dear Atul.

[snip]

 # Set the relaxation dispersion experiment type.
 relax_disp.exp_type(spectrum_id=id, exp_type='R1rho')
 - Well, the program needs to know which code-path to take. Not CPMG code. 
 :-)


 # Set the relaxation dispersion spin-lock field strength (nu1).
 relax_disp.spin_lock_field(spectrum_id=id, field=field)
 - Here: 'help(relax_disp.spin_lock_field)', show is that this should be in 
 Hz.
 - Let is review figure Fig1_Palmer_Massi_2006.png
 - This is the w_1 on S_x axis.
 - What is here put into relax is nu_1. This is then later converted
 to w_1, by multiplying with 2*pi.
 - It seems that you have: 'spin-lock amplitude' / nu_1 / 'spin-lock
 field' in column 4, while the the sample script has this in Column 3.

 # Set the spin-lock offset.
 relax_disp.spin_lock_offset(spectrum_id=id, offset=offset)
 - Here: 'help(relax_disp.spin_lock_offset)', show is that this should
 be in ppm.
 - I see you have the distance/position (in Hz)  of the spin-lock
 carrier in column 3. Values of 2100, 2728, ...  ... ...6500
 - Relax needs to know the position in ppm. Edward can give you a
 detailed description why we use ppm. It is related to minimise user
 error input.
 - You need to calculate this yourself.
 If you use NMRPipe, and look in 'fic.com', it could look like this
 var2pipe -in ./fid \
  -noaswap  \
   -xN  2044  -yN   256  \
   -xT  1022  -yT   128  \
   -xMODEComplex  -yMODE  Rance-Kay  \
   -xSW12001.200  -ySW 2659.928  \
   -xOBS 750.061  -yOBS  76.012  \
   -xCAR  4.7893  -yCAR 118.536  \
   -xLAB  HN  -yLAB N15  \
   -ndim   2  -aq2D  States  \
   -out ./test.fid -verb -ov

 Or try this script in relax:

 relax test.py
   test.py
 from math import pi
 from lib.physical_constants import return_gyromagnetic_ratio

 H_frq = 900.0e6
 print(The magnetic field strength as the proton frequency in Mega
 Hertz: %3.2f % (H_frq / 1.E6) )

 xOBS_Hz = H_frq
 B0_tesla =  xOBS_Hz / return_gyromagnetic_ratio(nucleus='1H') * 2.0 * pi
 print(BO in Tesla: %3.2f % B0_tesla)

 yOBS_N15_Hz = abs( xOBS_Hz / return_gyromagnetic_ratio(nucleus='1H') *
 return_gyromagnetic_ratio(nucleus='15N') )
 print(The precess frequency for 15N in MHz: %3.2f % (yOBS_N15_Hz / 1.E6) )

 offset_Hz = 2100.

 offset_ppm_N15 = offset_Hz / yOBS_N15_Hz * 1E6
 print(The offset ppm: %3.2f % (offset_ppm_N15) )

 # Position of carrier.
 yCAR_N15_ppm = 118.536
 print(The center position of the carrier: %3.2f % (yCAR_N15_ppm) )

 omega_rf_ppm = yCAR_N15_ppm + offset_ppm_N15
 print(The omega_rf in ppm: %3.2f % (omega_rf_ppm) )
 

This is correct, you will have have to convert to ppm values.  The
reason is simple, this is the most universal way of specifying the
position in the spectrum as it is field strength independent.  And it
matches the ppm units of the chemical shifts you will have loaded.
Some people measure Hz units from the centre of the spectrum, others
from the edge of the spectrum.  It often depends if you are a Varian,
Bruker, or Joel user.  But with ppm units, such issues do not need to
be handled within relax.

Regards,

Edward

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Re: field strength off-resonance R1rho constant relax time relaxation dispersion

[Edward d'Auvergne]

Hi Atul,

Again continuing from Troels' post at
http://thread.gmane.org/gmane.science.nmr.relax.user/1718/focus=1732.
Well, actually, as Troels fully covered all of you questions in more
detail than I could have provided, I don't have anything to add.  If
you have other questions, please don't hesitate to ask.

Regards,

Edward


On 21 August 2014 12:00, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:

[snip]

 relax_disp.relax_time(spectrum_id=id, time=relax_time)
 - This is used for the initial R2eff calculation, for exponential
 curve fitting.

 # Set the NMR field strength of the spectrum.
 spectrometer.frequency(id=id, frq=H_frq)
 - This is used for conversion between nucleus, etc.

 # Load the R1 data.
 relax_data.read(ri_id='500MHz', ri_type='R1', frq=500e6,
 file='R1_500MHz.out', dir=DATA_PATH, mol_name_col=1, res_num_col=2,
 res_name_col=3, spin_num_col=4, spin_name_col=5, data_col=6,
 error_col=7)
 - R1 needs to be loaded. This is because that R1 is part of the
 equations. :-) The next release of relax, will implement feature where
 R1 is fitted.
 Note, that fitting introduces another variable in the equations.

 # Read the chemical shift data.
 chemical_shift.read(file='ref_500MHz.list', dir=DATA_PATH)

 - This is needed to get the ppm position of the nucleus.
 - See now: http://www.nmr-relax.com/manual/Dispersion_model_summary.html
 - The average resonance in the rotating frame Omega(bar) = w_(bar) - w_rf.
 - Here w_bar is the chemical shift, and w_rf is the offset.
 - Let is review figure Fig1_Palmer_Massi_2006.png
 - This is the S_z axis.

 That should be it.

 If you have any questions, please don't hesitate to write again.

 If you need more help, consider writing a support request on the
 homepage tracker.
 - https://gna.org/support/?group=relax

 Add following information:
 # Please attach a system info file
 relax -i -t relax_i.txt

 # Please write up, which buttons you pushed, or attach your script.
 # Consider adding your data in sample format. Meaning that you
 delete all confidential information from the files, and only have 1-2
 residues left for testing.

 If you write such a support request, it it easier to share script files, and
 help other users.

 The benefits from such a support request is:
   - The information is available to all users, which can benefit
 others in same situation.
   - The information can be tracked back.
   - The relax manual can be expanded, to help future users in same situation.


 Good luck!

 Best
 Troels Emtekær Linnet
 PhD student
 Copenhagen University
 SBiNLab, 3-0-41
 Ole Maaloes Vej 5
 2200 Copenhagen N
 Tlf: +45 353-22083
 Lync Tlf: +45 353-30195

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Re: Relax - model free without a structure/PDB?

[Edward d'Auvergne]

Hi Ryan,

Welcome to the relax mailing lists!  I hope that the links Troels
posted were of help.  I am now back from holidays, hence the late
reply.  The problem you have, of not having a PDB file or 3D structure
has been encountered before.  For example searching the relax users
mailing list (http://dir.gmane.org/gmane.science.nmr.relax.user), you
may find:

http://thread.gmane.org/gmane.science.nmr.relax.user/472/focus=476

This was a long time ago, but from memory I made it possible to
perform a model-free analysis without having 3D structural
information.  However, you should be very, very careful about
artificial motions in the spherical diffusion model.  See the
following for a review of these fatal issues:

d'Auvergne E. J., Gooley P. R. (2007). Set theory formulation of
the model-free problem and the diffusion seeded model-free paradigm.
Mol. Biosyst., 3(7), 483-494. (http://dx.doi.org/10.1039/b702202f)

In summary - if you don't see the motion of the spherical model in the
local tm model, then it probably isn't real!

For the dipole-diploe interaction, you will need to set this up
differently.  As I am guessing that you are using the GUI interface,
just follow the instructions at
http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_relaxation_interactions.html.
You can skip or cancel the unit vector calculation part of the
dipole-dipole interaction wizard as this will just give a RelaxError.
But you will then have the dipole-dipole interaction set up.  Note
that this is performed in the script UI mode in the sample script
described at 
http://www.nmr-relax.com/manual/Single_model_free_model_script_mode_sample_script.html.
I hope this helps.

Regards,

Edward


On 31 July 2014 21:47, Ryan Lo rhl...@virginia.edu wrote:
 Hello,

  I'm also a new user of Relax.  I have a perhaps silly question.

  I'm studying a protein without a structure, and have processed my R1 R2
 relaxation data at 600 and 800 MHz using Relax. When I move to the
 Model-free analysis portion, I've followed the manual, and have tried
 changing the Protocol mode, as suggested:
  However if you are studying a system without a 3D structure,you can
 execute each individual component of the analysis byclicking on the
 “Change” button.

 However, Relax throws an error, saying

 Missing data.
 The set up is incomplete.
 Please check for the following missing information:
 Interatomic data (for the dipole-dipole interaction)

 Considering I don't have a PDB to read for the dipolar relaxation input, is
 there a way I can continue? Thank you all very much for your time. I look
 forward to hearing your response.

 From,
 Ryan
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Re: field strength off-resonance R1rho constant relax time relaxation dispersion

[Edward d'Auvergne]

Hi Atul,

I have just returned from holidays, hence my late reply.  However
Troels' reply should have fully addressed your questions and issues.
Is the analysis now working for you?  Note that the spin-lock
amplitude Omega_1 is the spin-lock field strength or nu_1, as you have
supplied (converted using the factor of 2*pi).  Tilt angles and
anything else the specific model requires are calculated from this and
the difference of the spin's chemical shift and the experiment
specific spin-lock offset.

Regards,

Edward




On 2 August 2014 09:52, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Dear Atul.

 I forgot one question.

 Do you have R1 data available?

 relax cannot currently do calculation without these measured values.
 relax_data.read(ri_id='R1', ri_type='R1',
 frq=cdp.spectrometer_frq_list[0], file= .)

 I am about to try to also make it possible to fit R1 values.
 sr #3135: Optimisation of the R1 relaxation rate for the off-resonance
 R1rho relaxation dispersion models.
 https://gna.org/support/?3135

 But that can take some weeks before it is implemented, and tested properly.

 Best
 Troels

 2014-08-02 9:47 GMT+02:00 Troels Emtekær Linnet tlin...@nmr-relax.com:
 Dear Atul.

 Welcome to the mailing list!

 This question is a very good one, and is not covered good enough in the 
 manual !

 There has been a question related to this question on the mailing list 
 recently.
 From Peixiang, at:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1654
 http://thread.gmane.org/gmane.science.nmr.relax.user/1666
 http://thread.gmane.org/gmane.science.nmr.relax.user/1667

 Try to go through these post first, to cover the background.
 Don't get to confused, I will give you the answer below. :-)

 By asking here on the public mailing list, your question will
 potentially help any other users who would
 have the same question. And it will help us to turn our attention to
 the manual lacking a tutorial for R1rho models.

 For example this mailing list can be viewed here:
 http://thread.gmane.org/gmane.science.nmr.relax.user

 And searches in same mail directory can be done here:
 http://dir.gmane.org/gmane.science.nmr.relax.user

 Your specific question is now listed here:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1718

 Edward can probably extend the your answer into details.
 I know, that he is on holiday for the next two weeks, so I can try to
 answer your question.

 I am a PhD student at the structural biology in Copenhagen, and have
 been working on the dispersion branch (CPMG and R1rho).
 So I will however do my best to try to help you in the meantime.

 # How to get help

 How to find help:
 The manual
 http://wiki.nmr-relax.com/Manual

 Related to: Relaxation Dispersion:
 http://www.nmr-relax.com/manual/Relaxation_dispersion.html
 http://www.nmr-relax.com/manual/Relaxation_dispersion_optimisation_theory.html
 http://www.nmr-relax.com/manual/Analysing_dispersion_in_prompt_script_UI_mode.html
 http://www.nmr-relax.com/manual/Dispersion_model_summary.html

 It seems we have a problem, that setting up R1rho experiments is not
 covered in well the manual.

 Then I see that you have found the folder with sample scripts.
 The sample script at:
 cat sample_scripts/relax_disp/R1rho_analysis.py

 Did you know, that you can get help to all the functions?

 You can start relax, and see the help information this way:
 relax
 help(sequence.read)
 help(spectrum.read_intensities)

 But what you are looking for is this:
 help(relax_disp.spin_lock_field)
 help(relax_disp.spin_lock_offset)

 Or go to the GUI, and in the top select:
 user functions (n-z) - relax_disp - spin_lock_field

 -

 Relax has something called system tests, which make sure that all
 functions of relax is kept when changing the code.

 Try opening the setup of one of these systemtests:
 gedit test_suite/system_tests/relax_disp.py

 And search for def setup_r1rho_kjaergaard.
 Skip all lines with:
 - self.assertEqual
 Delete all:
 - self.interpreter

 Here you can get another way to inspire you how to setup things.
 Test data resides in:
 cd test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/

 And have been analysed by:
 http://wiki.nmr-relax.com/Tutorial_for_Relaxation_dispersion_analysis_r1rho_fixed_time_recorded_on_varian_as_sequential_spectra#Intro

 So back to your question.
 You mention spin-lock amplitude.
 This is in relax called spin-lock field or  spin-lock field strength.

 If we set in the setup:

 -
 # In MHz.
 yOBS = 81.050
 # In ppm
 yCAR = 118.078
 centerPPM_N15 = yCAR
 ---

 # So for varian giving offset in Hertz, and relax wants in ppm:

 # Calculating the spin-lock offset in ppm, from offsets values provided in 
 Hz.
 frq_N15_Hz = yOBS * 1E6
 offset_ppm_N15 = float(deltadof2) / frq_N15_Hz * 1E6
 omega_rf_ppm = centerPPM_N15 + offset_ppm_N15

 # Set The spin-lock offset, omega_rf, in ppm.
 relax_disp.spin_lock_offset(spectrum_id=sp_id, offset=omega_rf_ppm)


 For this experiment, 

Re: dimer

[Edward d'Auvergne]

Hi Olena,

The time it takes for optimisation depends directly on the complexity
of motion in your system, the quality of the XH bond vector
orientations, the quality of your data (have you tried Sebastien
Morin's consistency testing analysis?), and how well the approximation
of a single, simple diffusion tensor is for your system.  These can
affect the total number of iterations of the protocol which can vary
between 2 and the maximum which defaults to 30.

Also the speed of the computer can have a large effect.  And having
access to a cluster and using Gary Thompson's multi-processor and
OpenMPI will have a huge effect on your calculation time.  The virtual
machine may also have a large effect.  The time could be between a few
minutes on a massive cluster with a rigid protein system to a few
weeks on the slowest system with complex dynamics and non-standard
Brownian diffusion.  But there are just too many factors involved to
know.  As Troels mentioned, you can run this directly on Windows.  It
is rather easy to set up a Python environment for relax on Windows and
I don't think you even need to be an administrator on certain systems.
This will probably give you more speed.

Regards,

Edward


On 18 August 2014 11:30, Olena Dobrovolska olena.dobrovol...@unibo.it wrote:
 Hi Edward,

  Yes, I solved this problem manually that day, i.e.I have started the 
 calculations.
  The problem was that I cut the DC files into the parts I was interested, 
 which caused the change of the format somehow.
  So I had to manually (omparing to the original file) make sure that the 
 spaces between the lines were identical.
  However, it has been running and already more than a week at the 'oblate' 
 stage. Is it normal? Or perhaps again there is  inconsistency with the fact 
 that I run it on the virtual machine Xubuntu installed on Windows platform?
  We will instal Relax on the new computer on Linux and then I will run once 
 again and see if the situation will change.
  Thanks for your prompt reply and a hint where to look.

  Regards,
  Olena

 
 From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of 
 Edward d'Auvergne [edw...@nmr-relax.com]
 Sent: 18 August 2014 08:39
 To: Troels Emtekær Linnet
 Cc: Olena Dobrovolska; Stefano Luciano Ciurli; relax-users@gna.org
 Subject: Re: dimer

 Hi Olena,

 I hope you have already solved this problem.  I have just returned
 from holidays, hence the late reply.  You will need to either obtain
 the latest relax sources as I haven't released a new relax version yet
 (see http://www.nmr-relax.com/download.html#Source_code_repository) or
 manually delete the spaces on all empty lines in all your files.  I
 have not done this myself, as I have modified relax to handle the
 spaces.  I do not know why there are spaces in your Bruker DC files,
 as none of the reference files Bruker sent me as we were
 collaboratively developing the relax-Bruker DC compatibility interface
 contained spaces (as can be found on the relax development mailing
 list, search for Neidig at
 http://dir.gmane.org/gmane.science.nmr.relax.devel).  So either this
 has been introduced in a newer Topspin version or Bruker DC file
 version or by some other means.

 Regards,

 Edward



 On 31 July 2014 18:49, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Dear Olena.

 If it has any interest, I just wish to turn your attention into,
 that it is possible to run relax on both Windows and Mac.

 I made these guide, when I tried a MS system,

 http://wiki.nmr-relax.com/Installation_windows_Python_x86-32_Visual_Studio_Express_for_Windows_Desktop

 And for mac.
 http://wiki.nmr-relax.com/Installation_mac_mavericks_os_x

 Best
 Troels

 2014-07-31 17:27 GMT+02:00 Olena Dobrovolska olena.dobrovol...@unibo.it:
 Dear Edward,

 I have doubled the spins for the NOE, T1, T2 files to run the analysis for 
 the dimer. The analysis took more than a month, and it was not completed 
 (stopped at the 'prolate' step), I believe because we were running it on a 
 virtual machine (Xubuntu), and not on a Linux computer, which we are going 
 to do.
 However, I wanted also to try running Relax on the separate protein parts. 
 The protein we are working with is composed of the domains arranged as 
 N-C-C-N. And I would like to run the first calculation for the C-C part, 
 for which I prepared the NOE, T1 and T2 files (output from DC) by doubling 
 the spins and cutting off the N-terminal parts (in the same way I have 
 prepared also the data for the N-terminal domain of the protein). However, 
 I can not load the data and therefore start the calculations. Whereas the 
 NOE files loading went well, for the T1 or T2 files upload Relax gives me 
 the following error message:

 relax bruker.read(ri_id='T1_700_N', 
 file='/home/olena/Desktop/BpUreE_domains/T1_UreE_700_Nterm.txt', dir=None)
 Opening the file '/home/olena/Desktop/BpUreE_domains/T1_UreE_700_Nterm.txt' 
 for reading.
 Traceback

Re: problem loading R1, R2 and nOe files for modelfree

[Edward d'Auvergne]

Hi Ravi,

For the new relax 3.2.3 version I announced last week
(http://article.gmane.org/gmane.science.nmr.relax.announce/57), have
you had the time to check if this fixes the problem?  If you would
like to receive these relax announcements, you can sign up for the
relax-announce mailing list at
https://mail.gna.org/listinfo/relax-announce/.  This email list
usually receives less than 10 emails per year.

Cheers,

Edward




On 2 July 2014 18:28, Ravi Pratap Barnwal ravi1...@gmail.com wrote:
 Hi Edward,
 I did try updating it using the svn command but it did not solve the issue.
 I probably need to wait for the newer version. When are you going to release
 that.


 regards
 ravi



 On Wed, Jul 2, 2014 at 12:29 AM, Edward d'Auvergne edw...@nmr-relax.com
 wrote:

 Hi,

 For reference, the bug report is at
 https://gna.org/bugs/index.php?22257.  I have now fixed the problem in
 the relax trunk.  The issue was exactly as I thought, and as I
 described in the bug report, but I needed confirmation that this was
 indeed the problem as your issue might have been a different bug.  If
 you have subversion installed on your system, then you can obtain the
 latest code using the command (via a terminal):

 svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk

 See http://www.nmr-relax.com/download.html#Source_code_repository and
 http://www.nmr-relax.com/manual/Latest_sources_relax_repositories.html
 for more details.  Otherwise you will have to wait for me to release
 relax 3.2.3 with this as well as a few other bug fixes.

 Cheers,

 Edward



 On 1 July 2014 23:29, Ravi Pratap Barnwal ravi1...@gmail.com wrote:
  Hi Edward,
  I have submitted the bug-report.
 
  regards
  ravi
 
 
  On Mon, Jun 30, 2014 at 12:54 AM, Edward d'Auvergne
  edw...@nmr-relax.com
  wrote:
 
  Hi Ravi,
 
  I think I have found what might be causing the problem.  But I'll wait
  until you have submitted a bug report before making any fixes and
  releasing a new version of relax, just to be sure that the problem you
  are seeing is the problem I am fixing.
 
  Cheers,
 
  Edward
 
 
  On 30 June 2014 08:28, Edward d'Auvergne edw...@nmr-relax.com wrote:
   Hi Ravi,
  
   I'm having difficulty replicating the issue.  Would you be able to
   create a bug report using the link
   https://gna.org/bugs/?func=additemgroup=relax ?  Cheers!  The more
   information you include the better.  For example the minimal steps
   require to trigger the bug.  You could also attach your screenshot
   there.  If there is enough detail for me to replicate the bug, then
   it
   usually takes me 5-10 minutes to fix it.  I could then release relax
   3.2.3 later this week with the fix.
  
   Cheers,
  
   Edward
  
  
   On 27 June 2014 21:04, Ravi Pratap Barnwal ravi1...@gmail.com
   wrote:
   Hi Edward,
   I am using version 3.2.2 on mac 10.8.5 (mountain lion). I am using
   GUI
   mode
   to run the relax. Here is the report from Tools- System
   Information
  
  
  
  
   relax 3.2.2
  
 Molecular dynamics by NMR data
   analysis
  
Copyright (C) 2001-2006 Edward
   d'Auvergne
Copyright (C) 2006-2014 the relax
   development
   team
  
   This is free software which you are welcome to modify and
   redistribute
   under
   the conditions of the
   GNU General Public License (GPL).  This program, including all
   modules,
   is
   licensed under the GPL
   and comes with absolutely no warranty.  For details type 'GPL'
   within
   the
   relax prompt.
  
   Assistance in using the relax prompt and scripting interface can be
   accessed
   by typing 'help' within
   the prompt.
  
   Processor fabric:  Uni-processor.
  
  
   relax sys_info()
  
   Hardware information:
   Machine: x86_64
   Processor:   i386
   Processor name:  Intel(R) Xeon(R) CPU   W3530  @
   2.80GHz
   Endianness:  little
   Total RAM size:  2048.0 Mb
   Total swap size: 11264.0 Mb
  
   Operating system information:
   System:  Darwin
   Release: 12.5.0
   Version: Darwin Kernel Version 12.5.0: Sun Sep
   29
   13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64
   Mac version: 10.8.5 (, , ) x86_64
   Distribution:
   Full platform string:Darwin-12.5.0-x86_64-i386-64bit
  
   Python information:
   Architecture:64bit
   Python version:  2.7.2
   Python branch:
   Python build:default, Apr  5 2012 18:46:15
   Python compiler: GCC 4.2.1 (Apple Inc. build 5666) (dot
   3)
   Libc version:
   Python implementation:   CPython
   Python revision:
   Python executable:
   /Applications/relax.app/Contents/MacOS/python
   Python flags:sys.flags(debug=0, py3k_warning=0

Re: problem loading R1, R2 and nOe files for modelfree

[Edward d'Auvergne]

Hi,

For reference, the bug report is at
https://gna.org/bugs/index.php?22257.  I have now fixed the problem in
the relax trunk.  The issue was exactly as I thought, and as I
described in the bug report, but I needed confirmation that this was
indeed the problem as your issue might have been a different bug.  If
you have subversion installed on your system, then you can obtain the
latest code using the command (via a terminal):

svn co http://svn.gna.org/svn/relax/trunk ./relax-trunk

See http://www.nmr-relax.com/download.html#Source_code_repository and
http://www.nmr-relax.com/manual/Latest_sources_relax_repositories.html
for more details.  Otherwise you will have to wait for me to release
relax 3.2.3 with this as well as a few other bug fixes.

Cheers,

Edward



On 1 July 2014 23:29, Ravi Pratap Barnwal ravi1...@gmail.com wrote:
 Hi Edward,
 I have submitted the bug-report.

 regards
 ravi


 On Mon, Jun 30, 2014 at 12:54 AM, Edward d'Auvergne edw...@nmr-relax.com
 wrote:

 Hi Ravi,

 I think I have found what might be causing the problem.  But I'll wait
 until you have submitted a bug report before making any fixes and
 releasing a new version of relax, just to be sure that the problem you
 are seeing is the problem I am fixing.

 Cheers,

 Edward


 On 30 June 2014 08:28, Edward d'Auvergne edw...@nmr-relax.com wrote:
  Hi Ravi,
 
  I'm having difficulty replicating the issue.  Would you be able to
  create a bug report using the link
  https://gna.org/bugs/?func=additemgroup=relax ?  Cheers!  The more
  information you include the better.  For example the minimal steps
  require to trigger the bug.  You could also attach your screenshot
  there.  If there is enough detail for me to replicate the bug, then it
  usually takes me 5-10 minutes to fix it.  I could then release relax
  3.2.3 later this week with the fix.
 
  Cheers,
 
  Edward
 
 
  On 27 June 2014 21:04, Ravi Pratap Barnwal ravi1...@gmail.com wrote:
  Hi Edward,
  I am using version 3.2.2 on mac 10.8.5 (mountain lion). I am using GUI
  mode
  to run the relax. Here is the report from Tools- System Information
 
 
 
 
  relax 3.2.2
 
Molecular dynamics by NMR data analysis
 
   Copyright (C) 2001-2006 Edward d'Auvergne
   Copyright (C) 2006-2014 the relax development
  team
 
  This is free software which you are welcome to modify and redistribute
  under
  the conditions of the
  GNU General Public License (GPL).  This program, including all modules,
  is
  licensed under the GPL
  and comes with absolutely no warranty.  For details type 'GPL' within
  the
  relax prompt.
 
  Assistance in using the relax prompt and scripting interface can be
  accessed
  by typing 'help' within
  the prompt.
 
  Processor fabric:  Uni-processor.
 
 
  relax sys_info()
 
  Hardware information:
  Machine: x86_64
  Processor:   i386
  Processor name:  Intel(R) Xeon(R) CPU   W3530  @
  2.80GHz
  Endianness:  little
  Total RAM size:  2048.0 Mb
  Total swap size: 11264.0 Mb
 
  Operating system information:
  System:  Darwin
  Release: 12.5.0
  Version: Darwin Kernel Version 12.5.0: Sun Sep 29
  13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64
  Mac version: 10.8.5 (, , ) x86_64
  Distribution:
  Full platform string:Darwin-12.5.0-x86_64-i386-64bit
 
  Python information:
  Architecture:64bit
  Python version:  2.7.2
  Python branch:
  Python build:default, Apr  5 2012 18:46:15
  Python compiler: GCC 4.2.1 (Apple Inc. build 5666) (dot 3)
  Libc version:
  Python implementation:   CPython
  Python revision:
  Python executable:
  /Applications/relax.app/Contents/MacOS/python
  Python flags:sys.flags(debug=0, py3k_warning=0,
  division_warning=0, division_new=0, inspect=0, interactive=0,
  optimize=1,
  dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
  tabcheck=0, verbose=0, unicode=0, bytes_warning=0)
  Python float info:
  sys.float_info(max=1.7976931348623157e+308,
  max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308,
  min_exp=-1021,
  min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
  radix=2, rounds=1)
  Python module path:
  ['/Applications/relax.app/Contents/Resources/lib/python27.zip',
  '/Applications/relax.app/Contents/Resources/lib/python2.7',
  '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-darwin',
  '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-mac',
 
  '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-mac/lib-scriptpackages',
  '/Applications/relax.app/Contents/Resources/lib/python2.7/lib-tk',
  '/Applications/relax.app/Contents

Re: problem loading R1, R2 and nOe files for modelfree

[Edward d'Auvergne]

Hi Ravi,

I think I have found what might be causing the problem.  But I'll wait
until you have submitted a bug report before making any fixes and
releasing a new version of relax, just to be sure that the problem you
are seeing is the problem I am fixing.

Cheers,

Edward


On 30 June 2014 08:28, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Hi Ravi,

 I'm having difficulty replicating the issue.  Would you be able to
 create a bug report using the link
 https://gna.org/bugs/?func=additemgroup=relax ?  Cheers!  The more
 information you include the better.  For example the minimal steps
 require to trigger the bug.  You could also attach your screenshot
 there.  If there is enough detail for me to replicate the bug, then it
 usually takes me 5-10 minutes to fix it.  I could then release relax
 3.2.3 later this week with the fix.

 Cheers,

 Edward


 On 27 June 2014 21:04, Ravi Pratap Barnwal ravi1...@gmail.com wrote:
 Hi Edward,
 I am using version 3.2.2 on mac 10.8.5 (mountain lion). I am using GUI mode
 to run the relax. Here is the report from Tools- System Information




 relax 3.2.2

   Molecular dynamics by NMR data analysis

  Copyright (C) 2001-2006 Edward d'Auvergne
  Copyright (C) 2006-2014 the relax development team

 This is free software which you are welcome to modify and redistribute under
 the conditions of the
 GNU General Public License (GPL).  This program, including all modules, is
 licensed under the GPL
 and comes with absolutely no warranty.  For details type 'GPL' within the
 relax prompt.

 Assistance in using the relax prompt and scripting interface can be accessed
 by typing 'help' within
 the prompt.

 Processor fabric:  Uni-processor.


 relax sys_info()

 Hardware information:
 Machine: x86_64
 Processor:   i386
 Processor name:  Intel(R) Xeon(R) CPU   W3530  @ 2.80GHz
 Endianness:  little
 Total RAM size:  2048.0 Mb
 Total swap size: 11264.0 Mb

 Operating system information:
 System:  Darwin
 Release: 12.5.0
 Version: Darwin Kernel Version 12.5.0: Sun Sep 29
 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64
 Mac version: 10.8.5 (, , ) x86_64
 Distribution:
 Full platform string:Darwin-12.5.0-x86_64-i386-64bit

 Python information:
 Architecture:64bit
 Python version:  2.7.2
 Python branch:
 Python build:default, Apr  5 2012 18:46:15
 Python compiler: GCC 4.2.1 (Apple Inc. build 5666) (dot 3)
 Libc version:
 Python implementation:   CPython
 Python revision:
 Python executable:   /Applications/relax.app/Contents/MacOS/python
 Python flags:sys.flags(debug=0, py3k_warning=0,
 division_warning=0, division_new=0, inspect=0, interactive=0, optimize=1,
 dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
 tabcheck=0, verbose=0, unicode=0, bytes_warning=0)
 Python float info:   sys.float_info(max=1.7976931348623157e+308,
 max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
 min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
 radix=2, rounds=1)
 Python module path:
 ['/Applications/relax.app/Contents/Resources/lib/python27.zip',
 '/Applications/relax.app/Contents/Resources/lib/python2.7',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-darwin',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-mac',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/plat-mac/lib-scriptpackages',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/lib-tk',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/lib-old',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/lib-dynload',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/site-packages',
 '/Applications/relax.app/Contents/Resources/lib/python2.7/site-packages']

 Python packages and modules (most are optional):

 Name   InstalledVersionPath
 minfx  True 1.0.6
 /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/minfx
 bmrblibTrue 1.0.3
 /Applications/relax.app/Contents/Resources/lib/python2.7/site-packages.zip/bmrblib
 numpy  True 1.6.1
 /Applications/relax.app/Contents/Resources/lib/python2.7/numpy
 scipy  True 0.10.1
 /Applications/relax.app/Contents/Resources/lib/python2.7/scipy
 wxPython   True 2.9.3.1 osx-cocoa (classic)
 /Applications/relax.app/Contents/Resources/lib/python2.7/wx
 matplotlib False
 mpi4py True 1.2.2
 /Applications

Re: R1rho RD analysis

[Edward d'Auvergne]

  0.509+/-0.006 seconds
http://wiki.nmr-relax.com/B14_full 0.488+/-0.006 seconds
http://wiki.nmr-relax.com/NS_CPMG_2-site_expanded  0.711+/-0.008 seconds
http://wiki.nmr-relax.com/NS_CPMG_2-site_3D   41.426+/-1.090 seconds
http://wiki.nmr-relax.com/NS_CPMG_2-site_3D_full  41.686+/-0.632 seconds
http://wiki.nmr-relax.com/NS_CPMG_2-site_star 31.209+/-0.635 seconds
http://wiki.nmr-relax.com/NS_CPMG_2-site_star_full30.933+/-0.496 seconds
http://wiki.nmr-relax.com/MMQ_CR72 0.863+/-0.007 seconds
http://wiki.nmr-relax.com/NS_MMQ_2-site   77.124+/-1.951 seconds
http://wiki.nmr-relax.com/NS_MMQ_3-site_linear83.364+/-1.075 seconds
http://wiki.nmr-relax.com/NS_MMQ_3-site   83.700+/-0.595 seconds
http://wiki.nmr-relax.com/M61  0.036+/-0.001 seconds
http://wiki.nmr-relax.com/DPL940.138+/-0.002 seconds
http://wiki.nmr-relax.com/TP02 0.172+/-0.002 seconds
http://wiki.nmr-relax.com/TAP030.294+/-0.002 seconds
http://wiki.nmr-relax.com/MP05 0.191+/-0.005 seconds
http://wiki.nmr-relax.com/NS_R1rho_2-site 33.027+/-0.549 seconds
http://wiki.nmr-relax.com/NS_R1rho_3-site_linear  64.863+/-1.602 seconds
http://wiki.nmr-relax.com/NS_R1rho_3-site 66.390+/-2.050 seconds

The full timing file with many more details can be seen at the
permanent link of
http://svn.gna.org/viewcvs/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_single.log?view=logpathrev=24364
or 
http://svn.gna.org/viewcvs/*checkout*/relax/branches/disp_spin_speed/test_suite/shared_data/dispersion/profiling/disp_profile_single.log?revision=24364pathrev=24364.

Regards,

Edward


P. S.  ATLAS can also be set up with numpy for even greater speed
(https://en.wikipedia.org/wiki/Automatically_Tuned_Linear_Algebra_Software).

On 27 June 2014 12:01, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Hi Troels,

 For reference for the relax users reading this, the abbreviations
 Troels used for the relaxation dispersion models can be decoded using
 the relax wiki page
 http://wiki.nmr-relax.com/Category:Relaxation_dispersion.

 Just a little heads-up.

 Within a week or two, we should be able to release a new version of relax.

 This update has focused on speed, recasting the data to higher
 dimensional numpy arrays, and
 moving the multiple dot operations out of the for loops.

 So we have quite much better speed now. :-)

 Troels, you just gave away the surprise of the relax 3.2.3 or 3.2.4
 release!  Note that relax was not particularly slow before these
 changes, but that you have taken far greater advantage of the
 BLAS/LAPACK libraries behind the numpy functions to make the
 dispersion models in relax super fast, especially when spins are
 clustered.  It's a pity we don't have the means to compare the
 optimisation target function speed between relax and other software to
 show how much faster relax now is, as the relax advantage of having a
 grid search to find the initial non-biased position for optimisation
 (a very important technique for optimisation that a number of other
 dispersion software do not provide) will give many relax users the
 incorrect impression that relax is slower than the other software.
 Though if relax is used on a cluster with OpenMPI, this is a
 non-issue.


 But we still have a bottleneck with numerical models, where doing the
 matrix exponential via eigenvalue decomposition is slow!
 Do any of you any experience with a faster method for doing matrix 
 exponential?

 These initial results shows that if you are going to use the R1rho
 2site model, you can expect:

 -R1rho
 100 single spins analysis:
 DPL94:  23.525+/-0.409 -   1.138+/-0.035,  20.676x 
 faster.
 TP02:   20.191+/-0.375 -   1.238+/-0.020,  16.308x 
 faster.
 TAP03:  31.993+/-0.235 -   1.956+/-0.025,  16.353x 
 faster.
 MP05:   24.892+/-0.354 -   1.431+/-0.014,  17.395x 
 faster.
 NS R1rho 2-site:   245.961+/-2.637 -  36.308+/-0.458,   6.774x 
 faster.

 Cluster of 100 spins analysis:
 DPL94:  23.872+/-0.505 -   0.145+/-0.002, 164.180x 
 faster.
 TP02:   20.445+/-0.411 -   0.172+/-0.004, 118.662x 
 faster.
 TAP03:  32.212+/-0.234 -   0.294+/-0.002, 109.714x 
 faster.
 MP05:   25.013+/-0.362 -   0.188+/-0.003, 132.834x 
 faster.
 NS R1rho 2-site:   246.024+/-3.724 -  33.119+/-0.320,   7.428x 
 faster.

 -CPMG
 100 single spins analysis:
 CR72:2.615+/-0.018 -   1.614+/-0.024,   1.621x 
 faster.
 CR72 full:   2.678+/-0.020 -   1.839+/-0.165,   1.456x 
 faster.
 IT99:1.837+/-0.030 -   0.881+/-0.010,   2.086x 
 faster.
 TSMFK01: 1.665+/-0.049

Re: problem loading R1, R2 and nOe files for modelfree

[Edward d'Auvergne]

Hi Ravi,

Which version of relax are you using and which operating system are
you running it on?  Are you using the newest 3.2.2 version?  Could you
run 'relax -i' or, in the GUI, select the 'Tools-System information'
menu item and the copy and paste the output into the body of a new
email?  Note that due to too much abuse of the system, attachments are
no longer allowed on the relax mailing lists to avoid excessive strain
on the open source infrastructure.  All attachments are filtered, i.e.
stripped from the message.  See your archived message at
http://article.gmane.org/gmane.science.nmr.relax.user/1695 for
example.  If you would like to share a file in such a situation, the
best solution is to create a bug report using the link
https://gna.org/bugs/?func=additemgroup=relax and to attach the file
there.  There are also support requests for non-bug related issues
where files can also be attached
(https://gna.org/support/?func=additemgroup=relax).

Cheers,

Edward


On 27 June 2014 00:50, Ravi Pratap Barnwal ravi1...@gmail.com wrote:
 Hi,
 I am encountering problem while loading R1,R2 and nOe values calculated for
 two different fields into relax (precompiled version 3.2.2) for mac 10.8.5.
 When i try to add the data and try to change the free format file
 settings for respective file, it is kind of hanging and does not proceed
 anywhere. My files are in the following format,
 3   GLY 1.814795542 0.090739777
 4   SER 2.267446596 0.11337233
 5   MET 2.621469801 0.13107349
 6   ASP 2.751590887 0.137579544


 Am i doing something wrong? I am following the protocol from this link,

 http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_data_pipe_initialisation.html

 I have attached a screen-shot for the problem. Any help is highly
 appreciated.

 regards
 ravi
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Re: Side chain dynamics

[Edward d'Auvergne]

Hi Mengjun,

Sorry for not getting back to you earlier.  The papers you mention are:

Oscar Millet and Anthony Mittermaier and David Baker and Lewis E.
Kay (2003)  The Effects of Mutations on Motions of Side-chains in
Protein L Studied by 2H NMR Dynamics and Scalar Couplings.  Journal of
Molecular Biology, 329, 551-563
(http://dx.doi.org/10.1016/S0022-2836(03)00471-6)

Eric Johnson and Walter J. Chazin and Mark Rance (2006)  Effects
of Calcium Binding on the Side-chain Methyl Dynamics of Calbindin D9k:
A 2H NMR Relaxation Study. Journal of Molecular Biology, 357,
1237-1252 (http://dx.doi.org/10.1016/j.jmb.2006.01.031).

The key here is that if these papers use the standard model-free
theory with no modifications, which I think they do though you need to
carefully check this, then this will work fine in relax where the
standard theory is implemented.  If the theory has been modified and
hence is not the original equations, then it might be time to learn
some computer programming ;)  But if you look at equation (1) of the
Rance paper, you will see that they measure 5 quadrupolar relaxation
rates.  If you have measured these, then you cannot use them in relax
yet.

There is currently no support in relax for quadrapolar relaxation
rates.  However it would be relatively easy to add.  Note that all of
the required infrastructure is in place.  The model-free spectral
density functions are all located in lib/spectral_densities.  Also
present are all model-free models, the highest quality optimisation
infrastructure, powerful model selection techniques, model elimination
infrastructure for failed models, the automated protocol that I came
up with for solving the convoluted diffusion tensor vs. internal
motion problem (though I don't know if this protocol would work if you
only measured Me deuterium relaxation and do not combine it with
backbone relaxation), powerfully data visualisation infrastructure,
etc.  The only work required is:

1)  Extending the list of input relaxation data types in the
relax_data.read user function.  This is trivial - the hard part is
deciding what to call these rates.
2)  Adding relevant functions to the relax library
lib/auto_relaxation/ modules to handle the additional rates.  This is
where the real work is.
3)  Added the quadrupolar coupling constant Q (or e2qQ/h) as a
model-free parameter that can be set via the value.set user function
(see 
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.parameter_object-pysrc.html#Model_free_params.__init__).
This requires one line of code.

The hardest part would be obtaining published test data.  That would
only require emailing one of the corresponding authors and explaining
what you would like to do, and the data in the Rance paper, especially
figure 4 appears to be the best for this.  The test data is then
turned into a system test - this is a mini-analysis used to check that
everything runs as expected.  I could do this in ~2 weeks of solid
work, but I don't have the time to allocate to such a task.  This
would also require the gradients and Hessians (1st and 2nd partial
derivatives) to be calculated for the relaxation rates:

http://www.nmr-relax.com/manual/Ri_theta_gradients.html
http://www.nmr-relax.com/manual/Ri_theta_Hessians.html
http://www.nmr-relax.com/manual/Ri_prime_theta_gradients.html
http://www.nmr-relax.com/manual/Ri_prime_theta_Hessians.html

This is rather trivial in Maxima, wxMaxima, Mathematica, or other
symbolic algebra systems.  However it is so simple that it could be
derived by hand in a few minutes.  If you would be interested in
adding this to relax, you could then mention this in your paper - that
you implemented quadrapolar relaxation rates in relax.  This could
then be added to the reference list in the citations chapter
(http://www.nmr-relax.com/manual/Model_free_analysis_references.html)
as well as a new section for citations at the start of the model-free
chapter (http://www.nmr-relax.com/manual/Model_free_analysis.html) so
that people using relax with such rates should then cite your paper.

Regards,

Edward

On 12 June 2014 14:35,  mengjun@mailbox.tu-berlin.de wrote:
 Hi Edward,

 Thank you so much. I would like to replicate the analysis in the publication
 The Effects of Mutations on Motions of Side-chains in Protein L Studied by
 2H NMR Dynamics and Scalar Couplings and Effects of Calcium Binding on the
 Side-chain Methyl Dynamics of Calbindin D9k: A 2H NMR Relaxation Study

 , where models LS2 and LS3 were used for fitting.

 Best regards,

 Mengjun





 Quoting mengjun@mailbox.tu-berlin.de:

 Hi Edward,
 There is some script in Relax software which can be used for analyzing
 side chain dynamics (R1 and R1r of deuterium in CH2D isotopomers)? Thank
 you.

 Best regards,

 Mengjun





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Re: R1rho RD analysis

[Edward d'Auvergne]

Hi Troels,

For reference for the relax users reading this, the abbreviations
Troels used for the relaxation dispersion models can be decoded using
the relax wiki page
http://wiki.nmr-relax.com/Category:Relaxation_dispersion.

 Just a little heads-up.

 Within a week or two, we should be able to release a new version of relax.

 This update has focused on speed, recasting the data to higher
 dimensional numpy arrays, and
 moving the multiple dot operations out of the for loops.

 So we have quite much better speed now. :-)

Troels, you just gave away the surprise of the relax 3.2.3 or 3.2.4
release!  Note that relax was not particularly slow before these
changes, but that you have taken far greater advantage of the
BLAS/LAPACK libraries behind the numpy functions to make the
dispersion models in relax super fast, especially when spins are
clustered.  It's a pity we don't have the means to compare the
optimisation target function speed between relax and other software to
show how much faster relax now is, as the relax advantage of having a
grid search to find the initial non-biased position for optimisation
(a very important technique for optimisation that a number of other
dispersion software do not provide) will give many relax users the
incorrect impression that relax is slower than the other software.
Though if relax is used on a cluster with OpenMPI, this is a
non-issue.


 But we still have a bottleneck with numerical models, where doing the
 matrix exponential via eigenvalue decomposition is slow!
 Do any of you any experience with a faster method for doing matrix 
 exponential?

 These initial results shows that if you are going to use the R1rho
 2site model, you can expect:

 -R1rho
 100 single spins analysis:
 DPL94:  23.525+/-0.409 -   1.138+/-0.035,  20.676x 
 faster.
 TP02:   20.191+/-0.375 -   1.238+/-0.020,  16.308x 
 faster.
 TAP03:  31.993+/-0.235 -   1.956+/-0.025,  16.353x 
 faster.
 MP05:   24.892+/-0.354 -   1.431+/-0.014,  17.395x 
 faster.
 NS R1rho 2-site:   245.961+/-2.637 -  36.308+/-0.458,   6.774x 
 faster.

 Cluster of 100 spins analysis:
 DPL94:  23.872+/-0.505 -   0.145+/-0.002, 164.180x 
 faster.
 TP02:   20.445+/-0.411 -   0.172+/-0.004, 118.662x 
 faster.
 TAP03:  32.212+/-0.234 -   0.294+/-0.002, 109.714x 
 faster.
 MP05:   25.013+/-0.362 -   0.188+/-0.003, 132.834x 
 faster.
 NS R1rho 2-site:   246.024+/-3.724 -  33.119+/-0.320,   7.428x 
 faster.

 -CPMG
 100 single spins analysis:
 CR72:2.615+/-0.018 -   1.614+/-0.024,   1.621x 
 faster.
 CR72 full:   2.678+/-0.020 -   1.839+/-0.165,   1.456x 
 faster.
 IT99:1.837+/-0.030 -   0.881+/-0.010,   2.086x 
 faster.
 TSMFK01: 1.665+/-0.049 -   0.742+/-0.007,   2.243x 
 faster.
 B14: 5.851+/-0.133 -   3.978+/-0.049,   1.471x 
 faster.
 B14 full:5.789+/-0.102 -   4.065+/-0.059,   1.424x 
 faster.
 NS CPMG 2-site expanded: 8.225+/-0.196 -   4.140+/-0.062,   1.987x 
 faster.
 NS CPMG 2-site 3D: 240.027+/-3.182 -  45.056+/-0.584,   5.327x 
 faster.
 NS CPMG 2-site 3D full:240.910+/-4.882 -  45.230+/-0.540,   5.326x 
 faster.
 NS CPMG 2-site star:   186.480+/-2.299 -  36.400+/-0.397,   5.123x 
 faster.
 NS CPMG 2-site star full:  187.111+/-2.791 -  36.745+/-0.689,   5.092x 
 faster.

 Cluster of 100 spins analysis:
 CR72:2.610+/-0.035 -   0.118+/-0.001,  22.138x 
 faster.
 CR72 full:   2.674+/-0.021 -   0.122+/-0.001,  21.882x 
 faster.
 IT99:0.018+/-0.000 -   0.009+/-0.000,
 2.044x faster. IT99: Cluster of only 1 spin analysis, since v. 3.2.2
 had a bug with clustering analysis.:
 TSMFK01: 1.691+/-0.091 -   0.039+/-0.000,  43.369x 
 faster.
 B14: 5.891+/-0.127 -   0.523+/-0.004,  11.264x 
 faster.
 B14 full:5.818+/-0.127 -   0.515+/-0.021,  11.295x 
 faster.
 NS CPMG 2-site expanded: 8.167+/-0.159 -   0.702+/-0.008,  11.638x 
 faster.
 NS CPMG 2-site 3D: 238.717+/-3.025 -  41.380+/-0.950,   5.769x 
 faster.
 NS CPMG 2-site 3D full:507.411+/-803.089 -  41.852+/-1.317,
 12.124x faster.
 NS CPMG 2-site star:   187.004+/-1.935 -  30.823+/-0.371,   6.067x 
 faster.
 NS CPMG 2-site star full:  187.852+/-2.698 -  30.882+/-0.671,   6.083x 
 faster.


There are a number of ways of computing the matrix exponential.
Avoiding eigenvalue decomposition is the essential key.  The Pade
approximation is probably the best, followed by one of the Taylor
series expansion approximations.  As I mentioned in a different post
to the relax-devel mailing list, this was used earlier in relax via
Scipy.  But I removed this and wrote my own algorithm using eigenvalue
decomposition as the Scipy 

Re: R1rho RD analysis

[Edward d'Auvergne]

Hi Peixiang,

Please see below:


 Congratulations about the new version of 3.2.2, I tried, it works well :)

Cheers.  If you notice any other problems or strange behaviour, please
don't hesitate to submit a bug report
(https://gna.org/bugs/?func=additemgroup=relax).  Then that problem
will likely be fixed for the next relax version.


 Still one question of using the different relaxation time periods.

 My R1rho RD experiment has different relaxation time periods, I could input 
 all the peaks by the loop.

 Then I fit with 'NS 2-site R1 model', they could also do the fitting and give 
 the results and also a nice fitting of the dispersion curve.
 Still I did not figure out, which Trelax is it using in the NS model in the 
 case of different relaxation time periods.
 Only the last relaxation time period? Then fit as fixed time experiment?

As this code was directly contributed by Paul Schanda and Dominique
Marion, and I'm guessing that their offices are not too far from yours
at the IBS, maybe you could ask them directly ;)  Well, it was Paul
who organised that the code be contributed to relax.  In reality the
original authors were Nikolai Skrynnikov and Martin Tollinger.  The
API documentation is also a useful resource for answering such
questions (http://www.nmr-relax.com/api/3.2/).  For this, see the
relax library documentation for that model:

http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-module.html

This documentation describes the origin and history of the code.  You
could even look at the source code for the direct implementation:

http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-pysrc.html

Trelax is the 'relax_time' argument here.  You can find all
implementation details in this API documentation.  Which relaxation
time would you suggest as being correct?  I'm actually no longer sure
which is being used.  And I'm not sure if the original code or even
the numeric model itself was designed to handle variable time data.


 Maybe I am the minority to use such time consuming experiments, so I always 
 have such strange questions ...

relax should still handle the situation.  Do you know if there is a
special treatment for the numerical models for such data?  Do you know
of a good citation?  Maybe the 'NS R1rho 2-site' model
(http://wiki.nmr-relax.com/NS_R1rho_2-site) is not suitable for
variable time data, and a different - and importantly published -
solution is required.  The analytic models do not use the relaxation
time value, so those are safe.  Hence, as a check, you should see very
similar results from the 'DPL94' model
(http://wiki.nmr-relax.com/DPL94) and the 'NS R1rho 2-site' model.  If
not, something is wrong.

If the 'NS R1rho 2-site' model is really only for fixed-time data,
then we should modify relax to raise a RelaxError when this model is
chosen for optimisation and the data is variable time.  As not many
people optimise numeric models to variable-time data, your input into
this question would be very valuable.  Cheers!


 Maybe another annoying question for the fix time people:
 Another question, does it necessary to check how mono-exponential about their 
 relaxation curve under certain rf-field? If not, how did they make sure they 
 can use the mono-exponential assumption to get R2eff by two points?

From what I've seen and heard, some people do check, but the majority
just assume that the curves will be mono-exponential and publish the
fixed-time data and results.  Such a check is probably much more
important for those collecting R1rho-type data rather than CPMG-type
data.  Anyway, maybe you should ask people in front of their posters
at conferences to get a better overview of what the field does.

Regards,

Edward



 Best,

 Peixiang




 On 05/19/2014 05:49 PM, Edward d'Auvergne wrote:

 Hi Peixiang,

 Welcome to the relax mailing lists!  The relaxation dispersion
 analysis implemented in relax is quite flexible, and the data you have
 is supported.  This is well documented in the relax manual which you
 should have with your copy of relax (the docs/relax.pdf file).  Have a
 look at section 'The R2eff model' in the dispersion chapter of the
 manual (http://www.nmr-relax.com/manual/R2eff_model.html),
 specifically the 'Variable relaxation period experiments' subsection.

 Unfortunately the sample scripts are all for the fixed time dispersion
 experiments.  However you could have a look at one of the scripts used
 for the test suite in relax:

 test_suite/system_tests/scripts/relax_disp/exp_fit.py

 This script is run in the test suite to ensue that the data you have
 will always be supported.  There are many more scripts in that
 directory which you might find interesting.  The 'r1rho_on_res_m61.py'
 script also involve an exponential fit with many different relaxation
 time periods.

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Re: R1rho RD analysis

[Edward d'Auvergne]

Hi Peixiang,

Actually, for comparison purposes for applying the 'NS R1rho 2-site'
model (http://wiki.nmr-relax.com/NS_R1rho_2-site) to variable-time
R1rho-type data, Art Palmer's MP05 model would be much better
(http://wiki.nmr-relax.com/MP05) than the DPL94 model
(http://wiki.nmr-relax.com/DPL94) as it is of much higher quality.
Andy Baldwin apparently has derived an even better analytic model,
especially when R20A and R20B are significantly different, see:

http://gna.org/support/?3155#comment0

and the discussions in the thread:

http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5447

and:

http://thread.gmane.org/gmane.science.nmr.relax.devel/5410/focus=5433

This last thread is about the B14 model (Baldwin 2014,
http://wiki.nmr-relax.com/B14) implemented in relax by Troels Linnet,
but there are mentions of Andy's R1rho model.  However the R1rho model
from Andy is not implemented in relax yet.  Do you have much
experience with variable-time R1rho numeric models?  Looking at the
code for where the relax_time variable comes from, it is not very
clear which relaxation time is being used:

http://www.nmr-relax.com/api/3.2/specific_analyses.relax_disp.data-module.html#loop_time

From the code itself:

http://www.nmr-relax.com/api/3.2/specific_analyses.relax_disp.data-pysrc.html#loop_time

it looks like this loop_time() function assumes fixed-time data and
hence only the first encountered time value for the given experiment,
magnetic field strength, offset, and dispersion point is used.  So
your expertise will be very useful for resolving this variable-time
R1rho numeric model problem!

Note that there are a few improvements to the R1rho models that are
yet to be implemented in relax:

http://thread.gmane.org/gmane.science.nmr.relax.devel/5414/focus=5808
http://www.nmr-relax.com/manual/do_dispersion_features_yet_be_implemented.html

Cheers,

Edward



On 11 June 2014 10:07, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Hi Peixiang,

 Please see below:


 Congratulations about the new version of 3.2.2, I tried, it works well :)

 Cheers.  If you notice any other problems or strange behaviour, please
 don't hesitate to submit a bug report
 (https://gna.org/bugs/?func=additemgroup=relax).  Then that problem
 will likely be fixed for the next relax version.


 Still one question of using the different relaxation time periods.

 My R1rho RD experiment has different relaxation time periods, I could input 
 all the peaks by the loop.

 Then I fit with 'NS 2-site R1 model', they could also do the fitting and 
 give the results and also a nice fitting of the dispersion curve.
 Still I did not figure out, which Trelax is it using in the NS model in the 
 case of different relaxation time periods.
 Only the last relaxation time period? Then fit as fixed time experiment?

 As this code was directly contributed by Paul Schanda and Dominique
 Marion, and I'm guessing that their offices are not too far from yours
 at the IBS, maybe you could ask them directly ;)  Well, it was Paul
 who organised that the code be contributed to relax.  In reality the
 original authors were Nikolai Skrynnikov and Martin Tollinger.  The
 API documentation is also a useful resource for answering such
 questions (http://www.nmr-relax.com/api/3.2/).  For this, see the
 relax library documentation for that model:

 http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-module.html

 This documentation describes the origin and history of the code.  You
 could even look at the source code for the direct implementation:

 http://www.nmr-relax.com/api/3.2/lib.dispersion.ns_r1rho_2site-pysrc.html

 Trelax is the 'relax_time' argument here.  You can find all
 implementation details in this API documentation.  Which relaxation
 time would you suggest as being correct?  I'm actually no longer sure
 which is being used.  And I'm not sure if the original code or even
 the numeric model itself was designed to handle variable time data.


 Maybe I am the minority to use such time consuming experiments, so I always 
 have such strange questions ...

 relax should still handle the situation.  Do you know if there is a
 special treatment for the numerical models for such data?  Do you know
 of a good citation?  Maybe the 'NS R1rho 2-site' model
 (http://wiki.nmr-relax.com/NS_R1rho_2-site) is not suitable for
 variable time data, and a different - and importantly published -
 solution is required.  The analytic models do not use the relaxation
 time value, so those are safe.  Hence, as a check, you should see very
 similar results from the 'DPL94' model
 (http://wiki.nmr-relax.com/DPL94) and the 'NS R1rho 2-site' model.  If
 not, something is wrong.

 If the 'NS R1rho 2-site' model is really only for fixed-time data,
 then we should modify relax to raise a RelaxError when this model is
 chosen for optimisation and the data is variable time.  As not many
 people optimise numeric models to variable-time data, your input

Re: dimer

[Edward d'Auvergne]

Hi Stefano,

For what has happened here, you need to open up your log file.  Did
you use relax with the --log or --tee command line options to capture
the messages?  If you go to the start of the messages, you will very
likely find RelaxWarnings which say something like deselecting the
spin due to missing {relaxation data; bond vector information; etc.}
or due to something else in the set up.  In relax, everything that
happens is sent to the log so you can always go back and see exactly
what happened.  I hope this solves your problem.

Regards,

Edward


On 10 June 2014 23:53, Stefano Luciano Ciurli stefano.ciu...@unibo.it wrote:
 Hi Edward, an additional question: in the output file I noticed that the last 
 four residues at the C-terminus, for which I provided relaxation data, are 
 not included. Any reason for it? (for the previous 9 residues we did not have 
 the assignment because they are not observed due to intermediate exchange 
 phenomena that broaden them too much to be visible, while the last four 
 residues are clearly visible and they appear to be very mobile, and yet, no 
 output from relax.
 Stefano

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Re: dimer

[Edward d'Auvergne]

Hi Stefano,

 It will be interesting to see the results in your final publication.

 well, same for us of course. However, this is the first time I approach this 
 problem, so I welcome any advice.

 Especially considering that the relaxation data you observe is the
 average of two states experiencing different global tumbling (the two
 vectors intersect different parts of a single Brownian diffusion
 tensor), but the assumption is made that they only sample one.

 the dimer is perfectly symmetric in solution, in the NMR time scale, as we 
 observe only a single peak per residue

For dimers, unfortunately I don't have much advice I can give.  The
only person who could we be the one who derives the correct
theoretical treatment of dimers in the future.  You may have avoided
the issue though if you have a perfectly symmetrical dimer.


 Maybe
 you should perform a full analysis on one monomer, and then another
 full analysis on the second, and compare.

 I am not sure that I understand your suggestion, as the two monomers are 
 inextricably bound

It won't give much, but the bond vectors orientations are different
between two monomers.  The superimposition is not perfect.  But, as we
have discussed before on the list, it will not do anything for the
theoretical problem, if you indeed do have a problem.  It will only
show you any small bond vector orientation artefacts.


 Are you sure there are no
 published theoretical treatments of such a situation?

 I am aware of relaxation studies on homodimeric proteins, but I am also quite 
 sure that the papers do not tackle the issue of the dimer and report the 
 relaxation data as for a monomeric protein; again, any advice is welcome.

I am also unaware of any theoretical treatment.  If you deposit your
dynamics data for your publication in the BMRB, via the relax export
functions, then this might open a door to allow a theoretician in the
future to use real data for solving this problem.  As for solving the
problem now and you are 100% sure that this is not already solved,
unless you would like to dive into quite complex theory, then there is
nothing we can do.  You could make a 1 line comment about the
deficiency in the manuscript, and make the statement that this is an
unsolved problem.

Anyway, the perfect symmetry might mean that the diffusion tensor as
seen in the reference frame of each monomer is identical, so that the
bond vectors in each experience the same 5 global correlation times
and hence the standard analysis will work perfectly.  If so, no
special theory is required.

Regards,

Edward

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Re: dimer

[Edward d'Auvergne]

Hi Stefano,

Please see below:

 thinking about it, and considering that we erroneously run Relax using the 
 full PDB for the homodimer but provided only the T1, T2 and NOE data for one 
 monomer, as output of Dynamics Center, could you tell us how to modify the 
 .txt files from Dynamics Center so that Relax thinks it has a full set of 
 data for the full homodimer? The PDB that we used has residues already 
 numbered consecutively from residue 1 to the last residue of the dimer.

In this setup, relax will only look at the first monomer.


 We really need to change the input files for T1, T2 and NOE in order to 
 decide which part of the protein we are looking at, but we would like to know 
 which parts of the output files from DC should be duplicated. If you want and 
 need it, I can send you the files in a private email to you only.

There is no need to send the files.  Do you have someone there who
knows scripting?  One option is to write a script (perl, Python, sed,
etc.) which adds 147 to the residue number for all parts of the Bruker
DC file.  Or maybe using the script at
http://thread.gmane.org/gmane.science.nmr.relax.user/1661/focus=1677
to renumber the PDB file will be sufficient.  Loading the two
molecules into relax and then loading the Bruker DC data might put the
data into the spin containers of both molecules, as the residue
numbers for both molecules will match.  This would have to be very
carefully checked as this is completely untested behaviour for relax.
You would also need to carefully look at the log messages.

If you would like me to make this last option 100% functional for
relax, I would recommend creating a support request and attaching your
Bruker DC files there - but they must be truncated to 1 or 2 residues.
You can randomise the data slightly too for complete secrecy, if you
wish.  I could then use this and the PDB file to create a relax system
test.  Having a system test allows me to fix things in relax in ~5 to
10 minutes.  The support request creation link is
http://gna.org/support/?func=additemgroup=relax.

Regards,

Edward

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Re: dimer

[Edward d'Auvergne]

Hi Stefano,

It will be interesting to see the results in your final publication.
Especially considering that the relaxation data you observe is the
average of two states experiencing different global tumbling (the two
vectors intersect different parts of a single Brownian diffusion
tensor), but the assumption is made that they only sample one.  Maybe
you should perform a full analysis on one monomer, and then another
full analysis on the second, and compare.  Are you sure there are no
published theoretical treatments of such a situation?

As for the PyMOL or MOLMOL macros, I've had a look at the PDB file you
attached to http://gna.org/support/?3110, and this might be difficult.
 Although both molecules are represented as different chains, the
residue numbers are not reset between the A to B transition:


ATOM   2437  HE1 HIS A 147  14.544 -14.592  44.384  1.00142.09   H
ATOM   2438  C   HIS A 147  15.448 -12.825  50.108  1.00142.09   C
ATOM   2439  O   HIS A 147  16.622 -12.826  50.563  1.00142.09   O
ATOM   2440  OXT HIS A 147  14.601 -13.730  50.336  1.00142.09   O
TER2441  HIS A 147
ATOM   2442  N   MET B 148  34.965   4.924 102.588  1.00 83.68   N
ATOM   2443  H   MET B 148  35.604   5.224 103.352  1.00 83.68   H
ATOM   2444  CA  MET B 148  33.567   5.117 103.004  1.00 83.68   C


Do you have the ability to renumber residues?  This is rather simple
in relax, though not so obvious as it plays directly with the relax
data store object and uses Python programming:


# Create a data pipe.
pipe.create('renumber', 'N-state')

# Load the original PDB as two molecules.
structure.read_pdb('BpUreE_apo_model_full.pdb')

# Renumber all residues of the second molecule directly in the
internal structural object.
for i in range(len(cdp.structure.structural_data[0].mol[1].res_num)):
cdp.structure.structural_data[0].mol[1].res_num[i] -= 147

# Write out the renumbered structure as a PDB file.
structure.write_pdb('BpUreE_apo_renumbered.pdb', force=True)


If the residues are all the same, then the PyMOL or MOLMOL macros
should apply to both structures.  I just had a look and the macros
from the model-free analysis apply to residue numbers:

http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.pymol-pysrc.html#Pymol.classic_colour
http://www.nmr-relax.com/api/3.2/specific_analyses.model_free.molmol-pysrc.html#Molmol.classic_colour

Regards,

Edward



On 5 June 2014 23:32, Stefano Luciano Ciurli stefano.ciu...@unibo.it wrote:
 Hi Edward,
 I reached the end of the calculation of our protein dimer, and everything 
 went smooth. We used two fields, and tomorrow I am about to start collecting 
 the third field data. I wonder how to make it so that the molmol or pymol 
 macros used to visualize the various parameters along the protein backbone 
 can be twisted so that these are applied to both monomers instead of just one.
 Cheers,
 Stefano

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Re:

[Edward d'Auvergne]

Dear Vineet,

The problem you are seeing is a simple bug - Dpar is simply being
displayed twice.  Could you please create a bug report for this?
Simply fill out the details at
https://gna.org/bugs/?func=additemgroup=relax.  I will then fix the
problem and the solution will be available with the next relax
release.  The bug report will be useful for other users

Cheers,

Edward


P. S.  I can already see the problem in the relax source code.  See if
you can see it too in the display() function at
http://www.nmr-relax.com/api/3.1/pipe_control.diffusion_tensor-pysrc.html#display.


On 14 May 2014 17:00, Panwalkar, Vineet v.panwal...@fz-juelich.de wrote:
 Dear users,

 I have recently carried out two seperate model-free analysis on a ~5 kDa 
 protein with relaxation data measured at 600, 800 and 900 MHz. I used the 
 fully automated analysis scripts for the analysis.

 In the first run, I used the lowest energy structure from my 15 structure 
 ensemble. I get an oblate diffusion tensor. When I read the results and ask 
 for diffusion_tensor.display() in relax, I get the table with all the data 
 which is as follows...

 Diffusion type   spheroid
   tm (s)4.63577e-09
   Diso (rad/s)  3.59523e+07
   Da (rad/s)   -3.36136e+07
   Dpar (rad/s)  1.35432e+07
   Dper (rad/s)  1.35432e+07
   Dratio   0.287196
   theta (rad)  0.633624
   phi (rad) 2.61738
   Fixed flag   True

 What is confusing me is that, even though the Dratio is 0.287196, the 
 individual Dpar and Dper values are exactly the same! I have seen the same 
 when I run relax on a complex of the 5 kDa protein and a 1.1 kDa peptide, 
 where relaxation data was recorded only for the protein.

 I ran another run, this time using the pdb file containing all the 15 lowest 
 energy structures. Analysis of the same relaxation data with this structure 
 gives me an ellipsoid diffusion model with following parameters..

 Diffusion type   ellipsoid
   tm (s)   4.63094e-09
   Diso (rad/s) 3.59898e+07
   Da (rad/s)2.4722e+07
   Dr  0.475806
   Dx (rad/s)   1.59863e+07
   Dy (rad/s)3.9512e+07
   Dz (rad/s)   5.24711e+07
   alpha (rad)  2.59643
   beta (rad) 2.087
   gamma (rad) 0.438009
   Fixed flag   True

 I remember reading an old post where Ed mentions that relax is not set up to 
 carry out analysis for residues with multiple NH bond vectors since it lies 
 in the model-free theory itself. In the same post it is also mentioned that 
 if that is the case then relax should give an error. Now, about 5 residues at 
 the N terminus and 2 at the C terminus of my 43 residue protein are 
 unstructured and show high backbone RMSD. It would be great if i get some 
 help regarding the understanding of why in such a case, there was no error 
 given from relax. And also, what measures are to be taken to run relax 
 analysis on such a protein using the 15 structure ensemble as an input 
 structure. Is this change from oblate to ellipsoid a case of over-estimation 
 of the diffusion properties occuring due to highly flexible termini in the 
 protein?

 Regards,

 Vineet


 
 
 Forschungszentrum Juelich GmbH
 52425 Juelich
 Sitz der Gesellschaft: Juelich
 Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
 Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
 Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
 Prof. Dr. Sebastian M. Schmidt
 
 

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Re: Re:

[Edward d'Auvergne]

Hi,

Alternatively, if your work email is going to reveal people's private
email addresses (the address behind my edward att nmr-relax dott com
email alias) as clear text on public mailings lists, do you have
another email system you can use?  The messages are archived
permanently at https://mail.gna.org/public/relax-users/,
http://www.mail-archive.com/relax-users@gna.org/,
http://dir.gmane.org/gmane.science.nmr.relax.user, and
http://marc.info/?l=relax-usersr=1w=2, so spam bots will easily find
the email addresses your email system is revealing.  Messages can
never be deleted from these archives - they are read only.

Cheers,

Edward



On 14 May 2014 18:38, Edward d'Auvergne edw...@nmr-relax.com wrote:
 Hi Vineet,

 Your mail software is still revealing my private email address to a
 public mailing list!  Please try changing your settings and responding
 just to me, to check if this is fixed.  Only once this setting is
 turned off would it be safe to respond to the mailing list.  Thanks.

 From your log messages, you are reading multiple files into relax.
 Can you complete a model-free analysis with this?  If so, could you
 created a bug report for this problem?  What does the log message look
 like when you get to the grid search or optimisation?

 Cheers,

 Edward




 On 14 May 2014 18:30, Panwalkar, Vineet v.panwal...@fz-juelich.de wrote:
 Hi Ed,

 I had a look at the log files. I reckon all the models within my ensemble 
 are added in. Unless I've understood the logs all wrong. Following is the 
 excerpt from the logs related to the PDB parser..

 relax structure.read_pdb(file=relax_input.pdb', dir=None, read_mol=None, 
 set_mol_name='protein', read_model=None, set_model_num=None, alt_loc=None, 
 merge=False)

 Internal relax PDB parser.
 Opening the file 'relax_input.pdb' for reading.
 Adding molecule 'protein' to model 1 (from the original molecule number 1 of 
 model 1)
 Adding molecule 'protein' to model 2 (from the original molecule number 1 of 
 model 2)
 Adding molecule ''protein' to model 3 (from the original molecule number 1 
 of model 3)
 Adding molecule ''protein' to model 4 (from the original molecule number 1 
 of model 4)
 Adding molecule 'protein' to model 5 (from the original molecule number 1 of 
 model 5)
 Adding molecule ''protein' to model 6 (from the original molecule number 1 
 of model 6)
 Adding molecule ''protein' to model 7 (from the original molecule number 1 
 of model 7)
 Adding molecule 'protein' to model 8 (from the original molecule number 1 of 
 model 8)
 Adding molecule ''protein' to model 9 (from the original molecule number 1 
 of model 9)
 Adding molecule ''protein' to model 10 (from the original molecule number 1 
 of model 10)
 Adding molecule ''protein' to model 11 (from the original molecule number 1 
 of model 11)
 Adding molecule ''protein' to model 12 (from the original molecule number 1 
 of model 12)
 Adding molecule ''protein' to model 13 (from the original molecule number 1 
 of model 13)
 Adding molecule ''protein' to model 14 (from the original molecule number 1 
 of model 14)
 Adding molecule ''protein' to model 15 (from the original molecule number 1 
 of model 15)

 Regards,

 Vineet

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Re: Re:

[Edward d'Auvergne]

Hi Vineet,

For the bug report, it would be great if you could create a truncated
data set and attach it to the report.  If you could truncate the PDB
files to 2-3 residues, and the relaxation data files to those same 2-3
residues, testing that the problem is still there, I'll then be able
to replicate the issue.  I could then add the data to the relax test
suite to make sure that the problem is thoroughly tested.  This also
often allows me to find a solution within 5 to 10 minutes.  You can
slightly randomise the data of this subset of spin if you wish to keep
it 100% confidential.

Do you use relax in the script UI mode?  Or the GUI?  How do you
perform the model-free analysis?

Cheers,

Edward




On 14 May 2014 19:05, Panwalkar, Vineet v.panwal...@fz-juelich.de wrote:
 Hi Ed,

 Model free analysis does complete after taking in all those structures. Every 
 single individual diffusion tensor model converges. The diffusion tensor data 
 in the earlier email was obtained after model free analysis was completed 
 using all 15 structures. I'll create a bug report regarding this.

 Cheers,

 Vineet
 


 Hi Vineet,

 Your mail software is still revealing my private email address to a
 public mailing list!  Please try changing your settings and responding
 just to me, to check if this is fixed.  Only once this setting is
 turned off would it be safe to respond to the mailing list.  Thanks.

 From your log messages, you are reading multiple files into relax.
 Can you complete a model-free analysis with this?  If so, could you
 created a bug report for this problem?  What does the log message look
 like when you get to the grid search or optimisation?

 Cheers,

 Edward





 Hi Ed,

 I had a look at the log files. I reckon all the models within my ensemble 
 are added in. Unless I've understood the logs all wrong. Following is the 
 excerpt from the logs related to the PDB parser..

 relax structure.read_pdb(file=relax_input.pdb', dir=None, read_mol=None, 
 set_mol_name='protein', read_model=None, set_model_num=None, alt_loc=None, 
 merge=False)

 Internal relax PDB parser.
 Opening the file 'relax_input.pdb' for reading.
 Adding molecule 'protein' to model 1 (from the original molecule number 1 of 
 model 1)
 Adding molecule 'protein' to model 2 (from the original molecule number 1 of 
 model 2)
 Adding molecule ''protein' to model 3 (from the original molecule number 1 
 of model 3)
 Adding molecule ''protein' to model 4 (from the original molecule number 1 
 of model 4)
 Adding molecule 'protein' to model 5 (from the original molecule number 1 of 
 model 5)
 Adding molecule ''protein' to model 6 (from the original molecule number 1 
 of model 6)
 Adding molecule ''protein' to model 7 (from the original molecule number 1 
 of model 7)
 Adding molecule 'protein' to model 8 (from the original molecule number 1 of 
 model 8)
 Adding molecule ''protein' to model 9 (from the original molecule number 1 
 of model 9)
 Adding molecule ''protein' to model 10 (from the original molecule number 1 
 of model 10)
 Adding molecule ''protein' to model 11 (from the original molecule number 1 
 of model 11)
 Adding molecule ''protein' to model 12 (from the original molecule number 1 
 of model 12)
 Adding molecule ''protein' to model 13 (from the original molecule number 1 
 of model 13)
 Adding molecule ''protein' to model 14 (from the original molecule number 1 
 of model 14)
 Adding molecule ''protein' to model 15 (from the original molecule number 1 
 of model 15)

 Regards,

 Vineet


 
 
 Forschungszentrum Juelich GmbH
 52425 Juelich
 Sitz der Gesellschaft: Juelich
 Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
 Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
 Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
 Prof. Dr. Sebastian M. Schmidt
 
 


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 relax-users@gna.org

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The hidden radian unit in relaxation dispersion.

[Edward d'Auvergne]

Hi,

The following is a copy of my post to the NESSY mailing list at
https://mail.gna.org/public/nessy-users/2014-03/msg1.html.  This
replicated here on the relax-users mailing list to be used as a
permanent relax reference (parts of it might be copied into the relax
wiki or manual in the future).  If you are interested in relaxation
dispersion, you might find the concepts useful for understanding the
Hertz vs. 1/s vs. rad/s vs. radian Hertz base units, especially for
the kex exchange parameter.  Below is the verbatim copy of the text.

Regards,

Edward


P. S.  Here is the text with a few minor corrections:



Hi Henriette,

Welcome to the NESSY mailing lists!  The problem you are seeing here
is not very well understood - even by the top experts in the field.
Many people are confused by the concept and it often results in
mistakes in papers.  To explain this, I will use the following
resources which I recommend that you read:

1)  The relaxation dispersion chapter of the user manual for the
software relax (http://www.nmr-relax.com) has a comprehensive table
listing all conceivable dispersion parameters and their base units
(http://download.gna.org/relax/manual/relax.pdf).  An online version
of the table can be seen at
http://www.nmr-relax.com/manual/Dispersion_model_summary.html.

2)  The hidden radian unit concept which I have explained at
http://wiki.nmr-relax.com/Hidden_radian_units.

3)  The unit analysis for the relaxation equations at
http://thread.gmane.org/gmane.science.nmr.relax.devel/1023/focus=1034.
 A similar unit analysis can be performed for kex, which I have
performed but not published or written anywhere.  This analysis works
for all models showing kex to have rad/s units, except for the IT99
model (http://wiki.nmr-relax.com/IT99).

4)  The software comparison table I produced for relax which compares
numerical results from most of the dispersion software available in
the field.  This is available with relax in the file
./test_suite/shared_data/
dispersion/software_comparison or online at
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/test_suite/shared_data/dispersion/software_comparison?revision=21873.


So, to begin, rad/s and 1/s are almost always the same thing in NMR as
almost everything we look at is rotational.  This is due to the hidden
radian unit concept (ref. 2).  Note that 1/s and Hz in NMR are most
definitely not the same thing and you need a factor of 2pi to convert
between them.  Just as a side note, 1/s is properly called radian
Hertz though this is not often used in the field.  By convention,
parameters with rad/s units are often called omega whereas parameter
with Hertz units are called nu.  Chemical exchange relates to chemical
shift, which is the change in how a nucleus spins in a magnetic field.
 The spinning means that chemical shift is a rotational process (which
interacts with the non-rotational external magnetic field and induced
magnetic fields for the electrons in the system, though these have
rotational fluctuations in the structural reference frame due to
Brownian and internal motions).  The Rex term which contributes to
relaxation hence has the units of rad/s.  This matches the units of
R1, R2, and sigma_NOE (see ref. 3), as well as the spectral density
functions governing standard relaxation.

In the case of kex, this is where a lot of confusion arises.  The
reason is because kex has both rad/s and Hertz units - there are
actually two kex parameters.  The first is the one which influences
the chemical shift - this has the radian unit.  The second is the
translational component of the mechanical process causing exchange -
the kinetic parameter of the process - this is non-rotational and
hence has Hertz units.  There is no factor of 2pi when converting
between the two!  A rotational process in rad/s or radian Hertz can
interact directly with a non-rotational process in Hertz with no
conversion factors.  For relaxation dispersion we assume both kex are
the same.  Therefore it is technically correct to present the single
numeric value with both 1/s and Hertz units (as well as rad/s and
radian Hertz units).  There is a case where kex can have rad^2 units
but I won't get into that (the rad^2/s units are mentioned at
https://en.wikipedia.org/wiki/Rotational_diffusion).

For a quick unit analysis, the CR72 dispersion model for CPMG-type
data is a simple starting point (http://wiki.nmr-relax.com/CR72).
From section 10.3.3 of the relax manual:

R2eff = 1/2 (R20A +  R02B + kex - 2*nu_CPMG*cosh^-1 (D+*cosh(eta+) -
D-*cos(eta-))).

The units of R2eff, R20A, and R20B are by definition rad/s.  Therefore
to add kex directly to these, kex must also have rad/s units (unit
analysis of the last term also produces rad/s, but I won't go into
that as it's too long).  For the M61 model for R1rho-type data
(http://wiki.nmr-relax.com/M61 and section 10.7.1 of the relax
manual):

R1rho = R1rho' + phi_ex*kex / (kex^2 + omega_e^2),

where:

phi_ex = pA*pB*delta_omega^2.

Here 

Re: Model-free analysis error

[Edward d'Auvergne]

Hi,

This addition was for the relaxation dispersion analysis and is in
section 10.14.2 Dispersion GUI mode - computation time.  The text
is:

The time required to complete these two analyses is highly dependent
on the computer being used as well as how many nodes can be used for
running the calculations parallelised with OpenMPI. On a large cluster
with many nodes both analyses should be completed in under an hour.
But when running the analyses without OpenMPI on old single core
computer, the analyses could take days and even up to a week.

For a model-free analysis, the computation time might range from 1 day
to 2 weeks, depending on how interesting the molecule is from a
dynamics perspective (the more dynamic, the more difficult the
problem) and if Gary Thompson's multi-processor with OpenMPI is used.

Regards,

Edward


On 26 March 2014 16:53, Troels Emtekær Linnet tlin...@nmr-relax.com wrote:
 Hi Ivanhoe.

 I remember that Edward added a section to the manual about running time, and
 probably somewhere on the relax mailing list that question is answered.

 But it depends on how many spins, computer power, and how many CPU.

 But I think that anything between a day and a week is expected (best guess
 is a week ? )
 Especially for model-free analysis.

 Best
 Troels



 2014-03-26 15:55 GMT+01:00 Ivanhoe Leung ivanhoe.le...@chem.ox.ac.uk:

 Dear Edward and Troels,

 Thanks for all your suggestions - they have all been really helpful. I
 have now added the errors onto the T1/T2/NOE lists (I use CCPNmr Analysis).

 Just one more question (maybe a stupid one) - how long does it take to do
 the full model free analysis (I just use the default settings on the GUI).
 Its been running for more than 6 hours now and the 'Incremental progress' is
 still showing less than 30% completion

 Thanks

 Ivan


 
 From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of
 Edward d'Auvergne [edw...@nmr-relax.com]
 Sent: 25 March 2014 18:03
 To: Ivanhoe Leung
 Cc: relax-users@gna.org
 Subject: Re: Model-free analysis error

 Hi Ivan and Troels,

 Continuing from
 http://thread.gmane.org/gmane.science.nmr.relax.devel/5263/focus=5268,
 the default error of 1.0 is important.  This causes the chi-square
 value to collapse into the sum of squared errors (SSE), making the
 analysis still possible.  However the real errors should really be
 provided at all times.  A model-free analysis requires the greatest
 precision and accuracy of all NMR analysis types.  Not providing
 errors, i.e. using crude errors of 1.0, for all data will really fubar
 your results (https://en.wikipedia.org/wiki/Military_slang#FUBAR).  If
 these are not available, please use the relaxation curve-fitting and
 steady-state NOE analyses in relax to properly calculate relaxation
 data errors from either replicated spectra or the base plane noise
 (see the 'rm' command in Sparky or the equivalent in other software).
 These peak intensity errors do not linearly map to the relaxation
 data, hence why different errors for all data points is rather
 important.

 Regards,

 Edward



 On 25 March 2014 18:35, Edward d'Auvergne edw...@nmr-relax.com wrote:
  Cheers!  I can confirm the problem - the identification of the @N and
  @H atom pairs takes a long, long time.  However it does successfully
  complete after a few minutes.  There are two problems I can identify.
  Solving the first will be the easiest.  From the saved state file that
  you uploaded, I can see that you have loaded all atoms of the PDB file
  into relax as nuclear spins.  For your analysis this is not necessary,
  just load the @N and @H atoms.  Then the interatom.define user
  function will operate much faster as then it will not need to loop
  over all these 1231 atoms (1231^2 times) but only the 296 @H and @N
  atoms.  See
  http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_setting_up_spin.html
  and
  http://www.nmr-relax.com/manual/GUI_mode_spins_from_structural_data.html
  for more details (the PDF version of the manual at
  http://download.gna.org/relax/manual/relax.pdf is of higher quality).
 
  The second problem is in relax.  There must be an inefficiency
  somewhere in the relax code which causes this to take so long.  I'll
  look and see if this function can be sped up, but it might require
  modifying the internal PDB reader in relax to automatically determine
  connected atoms for the standard protein/DNA/RNA residues.  Fixing
  this is a lot of work, so the first option might be fastest for you.
  As connected atoms in the protein were not automatically detected by
  the relax PDB reader, relax must first loop over each atoms to check
  for connections and for each it must then loop over all other atoms
  and determine if those atoms are within a certain short distance.  If
  so, it will consider the atoms to be bonded.  Because of these two
  nested loops, for 1231 atoms there would be 1231^2 = 1515361

Re: Model-free analysis error

[Edward d'Auvergne]

Hi Ivan,

If you could create a bug report using the link
https://gna.org/bugs/?func=additemgroup=relax, that would be
appreciated.  Please try to include as much information as possible.
The best would be if you could attach a truncated data set, the
minimum required to trigger the bug (slightly randomised if you would
like to keep it private).  If I can reproduce the bug myself, I can
normally have a fix for it within 5-10 minutes.  Oh, it would be good
to check that you are using the latest version of relax - currently
3.1.6 (http://www.nmr-relax.com/download.html) - just in case the bug
has already been fixed.

Cheers,

Edward



On 25 March 2014 15:33, Ivanhoe Leung ivanhoe.le...@chem.ox.ac.uk wrote:
 Dear Edward,

 I have now conducted measurements (T1, T2 and NOE) in two seperate fields 
 (600 and 700 MHz) as suggested in your previous email.

 I have upload six different files onto the Relaxation Data List. The data 
 is in the following format

 2 ALA 5.49631746729691 N
 3 ASP 3.74279511939516 N
 4 ASP 6.12594952217594 N
 6 SER 6.75812664729337 N

 However, after I click the Dipolar relaxation button, the programme freezes 
 up when I press Apply or Next.

 I encountered no problem with the other three buttons (CSA relaxation / X 
 isotope / H isotope)

 I wonder if it is because I am not supplying the right type of data to the 
 software, or if this is a python problem?

 Thanks and I hope to hear back from you soon!

 Ivan



 
 From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of 
 Edward d'Auvergne [edw...@nmr-relax.com]
 Sent: 10 February 2014 16:09
 To: Ivanhoe Leung
 Cc: relax-users@gna.org
 Subject: Re: Model-free analysis error

 Hi Ivan,

 To continue:

 On another note, I wonder if it is possible to modify the nmr-relax 
 programme so that I can do model-free analysis with data from only one field 
 strength? Alternatively, do you know of any programme (that can be installed 
 on Windows) that can do such analysis? My work focused mainly on small 
 molecule and ligand-based NMR and I have only just very recently started 
 looking in to protein dynamics so I am still experimentinng different 
 software and data treatment etc.

 Firstly, the subject of single field strength data has been discussed
 numerous times on this mailing list.  I would recommend you read my
 previous responses to questions relating to single field strength
 data, and look the other messages in those threads.  You will find
 these discussions quite informative and highly detailed:

 - Martin Ballaschk:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1409/focus=1438
 - Shantanu Bhattacharyya:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1367/focus=1369
 - Mengjun Xue:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1276/focus=1277
 - Fernando Amador: http://article.gmane.org/gmane.science.nmr.relax.user/84
 - Shantanu Bhattacharyya:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1086/focus=1087
 - Dhanasekaran Muthu:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1152/focus=1153
 - Vitaly Vostrikov:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1147/focus=1150
 - Aldino Viegas:
 http://thread.gmane.org/gmane.science.nmr.relax.user/1127/focus=1128
 - Pierre-Yves Savard:
 http://thread.gmane.org/gmane.science.nmr.relax.user/724/focus=725
 - Keith Constantine:
 http://thread.gmane.org/gmane.science.nmr.relax.user/513/focus=517
 - Clare-Louise Evans:
 http://thread.gmane.org/gmane.science.nmr.relax.user/326/focus=332
 - Hongyan Li:  
 http://thread.gmane.org/gmane.science.nmr.relax.devel/694/focus=701

 These will have lots of additional information.  This is just a
 selection of possibly the most useful messages.


 You will soon see that this is a complicated topic.  Note that relax
 is capable of performing 100% of the functionality of Modelfree4 (with
 or without the Fast-Modelfree GUI interface), Dasha, Tensor2, and
 DYNAMICS.  If you play with the optimisation settings you can even
 find identical results to within machine precision - relax can mimic
 these other softwares.

 The key is that the full analysis protocol is rather complicated -
 many people don't understand this - and that these softwares do not
 implement the full iterative protocol.  Therefore you either have to
 perform it manually or write a script to perform all of the steps.
 The protocol is described in the relax manual in figure 7.2
 (http://www.nmr-relax.com/manual/diffusion_seeded_paradigm.html).  In
 summary:

 a)  Find an initial diffusion tensor estimate (you can do this in
 relax by only using model m0).  This requires all non-mobile residues
 and side chain spins to be excluded, and this can be problematic.  See
 the d'Auvergne and Gooley, 2008b paper at
 http://dx.doi.org/10.1007/s10858-007-9213-3 for an example of the
 catastrophic failure that this initial estimate can result in.  Or the
 bacteriorhodopsin fragment of Korzhnev

Re: Model-free analysis error

[Edward d'Auvergne]

Cheers!  I can confirm the problem - the identification of the @N and
@H atom pairs takes a long, long time.  However it does successfully
complete after a few minutes.  There are two problems I can identify.
Solving the first will be the easiest.  From the saved state file that
you uploaded, I can see that you have loaded all atoms of the PDB file
into relax as nuclear spins.  For your analysis this is not necessary,
just load the @N and @H atoms.  Then the interatom.define user
function will operate much faster as then it will not need to loop
over all these 1231 atoms (1231^2 times) but only the 296 @H and @N
atoms.  See 
http://www.nmr-relax.com/manual/d_Auvergne_protocol_GUI_mode_setting_up_spin.html
and http://www.nmr-relax.com/manual/GUI_mode_spins_from_structural_data.html
for more details (the PDF version of the manual at
http://download.gna.org/relax/manual/relax.pdf is of higher quality).

The second problem is in relax.  There must be an inefficiency
somewhere in the relax code which causes this to take so long.  I'll
look and see if this function can be sped up, but it might require
modifying the internal PDB reader in relax to automatically determine
connected atoms for the standard protein/DNA/RNA residues.  Fixing
this is a lot of work, so the first option might be fastest for you.
As connected atoms in the protein were not automatically detected by
the relax PDB reader, relax must first loop over each atoms to check
for connections and for each it must then loop over all other atoms
and determine if those atoms are within a certain short distance.  If
so, it will consider the atoms to be bonded.  Because of these two
nested loops, for 1231 atoms there would be 1231^2 = 1515361
interatomic distance checks.  This is why it is slow.  For just the @N
and @H spins the number of checks would be ~20 times less.

Regards,

Edward


P. S.  For any relax developers out there, the fix is to support the
standard PDB atom naming in the Chemical Component Dictionary, as
described in http://www.wwpdb.org/documentation/format33/sect9.html#ATOM
and found at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/.  The ATOM
records in a PDB file must conform to this nomenclature and the given
CONECT records.  All the definitions are in the single file
ftp://ftp.wwpdb.org/pub/pdb/data/monomers/het_dictionary.txt.  For
example to see glycine, search for HETGLY.  The number of spaces
is essential here.  We could add the standard amino acid HET
dictionaries to relax and use the CONECT records in these to bond all
atoms together.  Some problems are that in X-ray structures certain
random atoms will be missing and that encountering non-standard or
modified amino acids is not uncommon.  Therefore the distance-based
algorithm would be always needed as a fallback if the relax PDB reader
does not find connected atoms for a given atom.



On 25 March 2014 16:34, Ivanhoe Leung ivanhoe.le...@chem.ox.ac.uk wrote:
 Dear Edward,

 I have submitted a bug report as requested

 https://gna.org/bugs/index.php?21862

 Thanks

 Ivan


 
 From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of 
 Edward d'Auvergne [edw...@nmr-relax.com]
 Sent: 25 March 2014 14:43
 To: Ivanhoe Leung
 Cc: relax-users@gna.org
 Subject: Re: Model-free analysis error

 Hi Ivan,

 If you could create a bug report using the link
 https://gna.org/bugs/?func=additemgroup=relax, that would be
 appreciated.  Please try to include as much information as possible.
 The best would be if you could attach a truncated data set, the
 minimum required to trigger the bug (slightly randomised if you would
 like to keep it private).  If I can reproduce the bug myself, I can
 normally have a fix for it within 5-10 minutes.  Oh, it would be good
 to check that you are using the latest version of relax - currently
 3.1.6 (http://www.nmr-relax.com/download.html) - just in case the bug
 has already been fixed.

 Cheers,

 Edward



 On 25 March 2014 15:33, Ivanhoe Leung ivanhoe.le...@chem.ox.ac.uk wrote:
 Dear Edward,

 I have now conducted measurements (T1, T2 and NOE) in two seperate fields 
 (600 and 700 MHz) as suggested in your previous email.

 I have upload six different files onto the Relaxation Data List. The data 
 is in the following format

 2 ALA 5.49631746729691 N
 3 ASP 3.74279511939516 N
 4 ASP 6.12594952217594 N
 6 SER 6.75812664729337 N

 However, after I click the Dipolar relaxation button, the programme 
 freezes up when I press Apply or Next.

 I encountered no problem with the other three buttons (CSA relaxation / X 
 isotope / H isotope)

 I wonder if it is because I am not supplying the right type of data to the 
 software, or if this is a python problem?

 Thanks and I hope to hear back from you soon!

 Ivan



 
 From: edward.dauver...@gmail.com [edward.dauver...@gmail.com] on behalf of 
 Edward d'Auvergne [edw...@nmr-relax.com]
 Sent: 10 February 2014 16:09

Re: Processing again

[Edward d'Auvergne]

Hi Martin,

This is a difficult question to answer.  From memory, linear
prediction has been mentioned in one or two of the hundreds of
model-free papers published to date.  However I cannot remember which
papers these would be.  And it is probably just a single line in the
back of a discussion somewhere.  By searching through my collection of
papers, I found the following more detailed reference:

N. J. Skelton, A. G. Palmer III, M. Akke, J. Kördel, M. Rance, and W.
J. Chazin, J. Magn. Reson. B 102, 253 (1993).

This is probably the most detailed study of linear prediction in NMR
relaxation, but I would not call it comprehensive.  As far as I am
aware, there is no systematic study on the effects of linear
prediction on a dynamics analysis.  For example what happens with
different levels of spectral data truncation, different number of
linear prediction coefficients, linear prediction in different
dimensions, as well as some of the other features of linear prediction
not implemented in NMRPipe.  It is well known that linear prediction
can introduce artifacts, however how this translates into relaxation
data or, more importantly, the model-free parameters is completely
unknown.  The problem with dynamics in NMR is that this requires the
highest precision and highest quality data possible - far greater than
any other NMR technique.  And therein lies the problem - without a
comprehensive study of how linear prediction affects the final
dynamics, you can never know what problems or artifacts that might
introduce.  And such artifacts may not be distinguishable from real
results.  Such a study could probably be published as a standalone
paper.

Anyway, you should probably look at performing the same types of
testing as in the above reference if you would like to get into linear
prediction.  You should also try processing without window functions,
as well as processing without the Fourier transform in the indirect
dimension to understand the level of truncation you have in the base
data.  Then if the Lorenzian to Gaussian window function amplifies the
truncation too much, then it should be dropped.  I usually use the
NMRPipe GM in the direct dimension and the 60 degree shifted sine
squared bell in the indirect, as I mention in the relax manual
(http://www.nmr-relax.com/manual/Spectral_processing.html).  If you
have truncation in the direct dimension and are not working with small
organic molecules, something is strange (even with small molecules it
would be strange).  You can see this if you process without any window
functions, linear prediction, baseplane corrections, and the Fourier
transform in the direct dimension.  I hope some of this helps.

Regards,

Edward


On 19 March 2014 15:53, Martin Ballaschk ballas...@fmp-berlin.de wrote:
 Hi Edward and relax-users,

 I was again thinking about the ideal processing strategy of my R1/R2 
 relaxation and HetNOE planes. Routinely in the past, I used the Topspin 
 Sine-Bell functions and linear prediction for resolution enhancement in the 
 indirect dimension. Now, I use NMRpipe with Lorentz-to-Gauss windows, but 
 with my collected data, I hardly get the needed resolution without having 
 severe truncation artifacts from my strong peaks wich contaminate 
 neighbouring peaks' intensities.

 The latter issue is why I don't use two sets of processing parameters (one 
 for intense and one for weak peaks), but fiddle around with overlapping peaks.

 I know that you advise to avoid linar prediction, but after reading 
 http://spin.niddk.nih.gov/NMRPipe/ref/nmrpipe/lp.html I have the impression 
 that LP could help ease the problem of truncation artifacts. I also did some 
 literature searching, but I didn't find anything about LP making peak height 
 measurements unreliable.

 I remember we discussed that during your visit, and I showed you the graphs 
 where I compared rates calculated from spectra without LP vs. rates from 
 spectra where the same number of points was added by LP. Maybe you remember, 
 there was no visible bias, but rates with large errors also became larger.

 So what again is the reason to not use LP for relaxation series?

 Cheers,
 Martin
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