mimic: intensity_generic();
> intensity_nmrview(); intensity_sparky(); intensity_xeasy(). If you
> would like to give it a try (it really doesn't matter what happens),
> then questions and the basic design can be discussed on the
> relax-devel mailing list.
>
> Regards,
Hi All,
Does relax accept input data from nmrpipe peak lists and, more
specifically, using the nlinls example provided with the nmrpipe
package? If not, are there a set of scripts or procedures someone can
point me to that imports xeasy or nmrview data, so I can copy-and-
modify these acco
for reading.
Perhaps you should attach the input script text as well as the output
text?
Doug
On Nov 9, 2008, at 5:45 PM, Tyler Reddy wrote:
> It looks like both problems were already fixed in my script, so it
> must be
> something else?
>
>
> Quoting Douglas Kojetin <[E
I made the following changes to the distributed latex_mf_table.py
file, and it seemed to work OK.
% diff updated_latex_mf_table.py old_latex_mf_table.py
42c42
< RESULTS_FILE = 'final/results.bz2'
---
> RESULTS_FILE = 'final'
171c171
< for spin, spin_id in spin_loop(return_id=True):
---
I see a similar bug that occurs right after the 'init' round.
Doug
On Oct 24, 2008, at 9:52 AM, Edward d'Auvergne wrote:
> Hi,
>
> This is a strange bug if it only occurred in the second round. I
> can't see what the problem is right now so I will have to think about
> this one for a bit. In
Hi All,
Is it necessary to have residues names (e.g. ALA) present in relax
input files, as the residue numbers should be sufficient to keep track
of the information? If it is not necessary, how can I configure the
full_analysis protocol/script (or others) to play nicely with input
files t
difference.
>
> That being said, this problem should not occur. But as I cannot do
> anything with the limited information, you may need to hunt down where
> the problem lies yourself (whether in relax, the operation of relax,
> the use of the quadric_diffusion program, or elsewh
tion data type and
> field strength will be very important. I would even be wary using 5
> data sets, especially if the missing data set is the higher-field NOE.
> So I would never recommend using 4 data sets.
>
> Regards,
>
> Edward
>
>
> On Jan 10, 2008 8:12 PM, Dou
was released
> prior to the redesign and almost everything should work. I'm assuming
> this all relates to my response at
> https://mail.gna.org/public/relax-users/2007-12/msg5.html (which
> is part of the thread started by your post at
> https://mail.gna.org/public/relax-us
u do want
> to play with the current code, note that the name 'run' has been
> replaced by the name 'pipe' and that the concept of a data pipe has
> been introduced so that the pipe name is not passed into each user
> function. That user functions apply automati
nt code, note that the name 'run' has been
> replaced by the name 'pipe' and that the concept of a data pipe has
> been introduced so that the pipe name is not passed into each user
> function. That user functions apply automatically to the 'current'
> da
Hi All,
When trying to use relax 1.3 (current svn version), I see the
following error when trying to use run.create():
% /usr/local/relax/1.3/relax
ImportError: relaxation curve fitting is unavailible, try compiling
the C modules.
relax repository che
A question re: unresolved residues. Is it necessary to list
unresolved residues in this file if no data was supplied for these
residues? Example r1 file (made up):
1
2
3 2.7114 0.05
4. 2.6151 0.04
Do residues 1 and 2 need to be listed in the unresolved file?
Thanks,
Doug
On Jan 10, 2008
20 iterations, to the
> universal solution using the looping procedure. For a published
> example of this type of failure, see the section titled "Failure of
> the diffusion seeded paradigm" in the previous link to the
> "Optimisation of NMR dynamic models II"
Hi All,
I am working with five relaxation data sets (r1, r2 and noe at 400
MHz; r1 and r2 and 600 MHz), and therefore cannot use the
full_analysis.py protocol. I have obtained estimates for tm,
Dratio, theta and phi using Art Palmer's quadric_diffusion program.
I modified the full_anal
r (this is an estimate
> as many assumptions about the internal motions are made and mobile
> residues should be filtered out first). Note though that this
> protocol minimally requires 4 relaxation data sets and optimally 6,
> hence to use it you cannot avoid collecting at multiple field
Hi,
In the following post [https://mail.gna.org/public/relax-users/
2007-05/msg9.html], Edward said that relax could be used to
estimate the diffusion tensor parameters (instead of using the
program Tensor). Does this protocol already exist in the form of a
python script? If not, coul
Hi All,
Quick question. I would just like to confirm if the Euler angles
alpha, beta, gamma or the theta and phi angles in the case of a
spheroid diffusion tensor are for the transformation of a vector from
the diffusion axes reference frame to the PDB reference frame (as
opposed to the o
depending on how you look at these
> scripts, be careful and maybe remove any line wrapping. I hope you
> find
> this useful.
>
> Regards,
>
> Edward
>
>
>
> On Mon, 2007-12-03 at 12:26 -0500, Douglas Kojetin wrote:
>> Hi Edward,
>>
>>
Hi Edward,
Is a relax script available that creates a PyMOL (or MOLMOL)
structure figure of the NH bond vector orientations, as shown in your
dissertation (Figure 7.8; page 252)?
Thanks,
Doug
___
relax (http://nmr-relax.com)
This is the relax-user
bug report, and
> attach a
> save state file from between the monte_carlo.initial_values() and the
> minimise() user functions.
>
> Cheers,
>
> Edward
>
>
> On Sat, 2007-11-17 at 12:44 -0500, Douglas Kojetin wrote:
>> Hi,
>>
>> I am running the final
Hi,
I am running the final optimization for the full_analysis.py
protocol, and the minimize call is reporting something I've never
encountered before:
...snip
The model from the run 'ellipsoid' has been selected.
relax> fix(run='final', element='diff', fixed=1)
relax> monte_carlo.setup(run=
ision being used) I will be able to head straight to the problem.
Thanks,
Edward
On 10/26/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
Hi Edward,
I've included the output from the log below, which is produced if
the
aforementioned lines are left commented out. If I uncomme
te
> between the run.create() and eliminate() user functions, that would be
> very useful. With the save state (and the relax version or SVN
> revision being used) I will be able to head straight to the problem.
>
> Thanks,
>
> Edward
>
>
>
> On 10/26/07, Douglas
response
> to this removal such that this test of spin system selection is not
> necessary. This important function solely determines what type of
> model-free analysis is being executed - local tm, diffusion tensor
> optimisation, model-free optimisation for a single spin, or
> optimisation
Hi,
The following comment is present on line 1021 in the specifc_fns/
model-free.py file of the 1.2 svn version of relax:
1021# This code causes a bug after model elimination if
the model has been eliminated (select = 0).
1022#if not self.relax.data.res[self.run][i].sel
Hi,
How important is precision for the input relaxation data (r1, r2,
noe) for relax analysis? My values were calculated using curvefit,
with values using 4 decimal places. On the other hand, relax curve
fitting produces rates with many more decimal places (16).
Thanks,
Doug
as you say, there could be other levels of queuing (that
> people more
> familiar with this topic than me could propose)...
>
> Ciao
>
>
> Séb
>
>
>
> Selon Douglas Kojetin <[EMAIL PROTECTED]>, 24.10.2007:
>
>> Hi,
>>
>> I think it would b
tion and also be in the background... A run would
start when the previous run would finish or crash.
This ain't perfect but is it worth spending time to modify the code
when a command line like this one can do the same thing ?
Let me know what you think.
Cheers
Séb
Douglas K
seful...
I would suggest you submit a patch to [EMAIL PROTECTED] to add
this feature as an option the user can activate or not depending on
its needs...
Cheers !
Séb :)
Douglas Kojetin wrote:
I guess I could also mentione that I've 'hacked' the
full_analysis.py script t
useful.
Doug
On Oct 22, 2007, at 4:22 PM, Sebastien Morin wrote:
Hi Doug !
Great !
I didn't know about that feature (and some others that "relax -
help" outputs)...
Séb :)
Douglas Kojetin wrote:
Hi Séb,
I've been using the -t flag creating one large log, so I t
Hi Séb,
I've been using the -t flag creating one large log, so I think this:
For analysis where some kind of looping is done (like here), the
logs could be separated into different steps. For the
full_analysis.py script, logging could be done independantly for
each round and added to the o
ve different residues in two different iterations of
> full_analysis.py then this error is much more severe and belongs
> elsewhere other than in the convergence tests.
>
> Cheers,
>
> Edward
>
>
>
> On 9/18/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> Hi
roblems with the dictionary ordering. I would
> prefer that this section not be present in the patch. If someone does
> have different residues in two different iterations of
> full_analysis.py then this error is much more severe and belongs
> elsewhere other than in the convergenc
nt residues in two different iterations of
> full_analysis.py then this error is much more severe and belongs
> elsewhere other than in the convergence tests.
>
> Cheers,
>
> Edward
>
>
>
> On 9/18/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> Hi Edward,
&g
gt; changes in a patch file which I can then check and commit to the
> repository with your name attached.
>
> Thanks,
>
> Edward
>
>
> On 9/17/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> As a followup, my changes to full_analysis.py solved my problem. I
>> wi
how
> you report the changes is up to you. If you change a checked out copy
> of the SVN repository and type 'svn diff > patch', you'll get the
> changes in a patch file which I can then check and commit to the
> repository with your name attached.
>
> Thanks,
&
in response to your original post
> (https://mail.gna.org/public/relax-users/2007-06/msg4.html,
> Message-id: <[EMAIL PROTECTED]>).
>
> I have a few more points about the tests you have done but to work out
> what is happening with the printouts, it would be very useful to ha
html,
> Message-id: <[EMAIL PROTECTED]>).
>
> I have a few more points about the tests you have done but to work out
> what is happening with the printouts, it would be very useful to have
> your modified 'full_analysis.py' script attached.
>
>
>
> On 9/17/07, Douglas Koj
public/relax-users/2007-07/msg1.html
> (Message-id:
> <[EMAIL PROTECTED]>)
> in response to your original post
> (https://mail.gna.org/public/relax-users/2007-06/msg4.html,
> Message-id: <[EMAIL PROTECTED]>).
>
> I have a few more points about the tests you have
Hi,
I'm unsure if this is a bug in full_analysis.py, in the internal
relax code, or user error. The optimization of the 'sphere' model
will not converge, now after 160+ rounds. The chi-squared test has
converged (long, long ago):
"" from output
Chi-squared test:
chi
Hi All,
Is there example/test-suite relaxation data (either distributed with
relax or some other standard data) that one can use to determine if
the full_analysis.py script is working properly?
Thanks,
Doug
___
relax (http://nmr-relax.com)
This is
the
> bug report in the SVN commit messages.
>
> Cheers,
>
> Edward
>
>
> On 8/29/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> Hi Edward,
>>
>> I am just picking back up on my relaxation analysis, and noticed that
>>
le to create a bug
> report for this issue? Thanks. There are three places in the
> 'convergence()' function in which this failure will occur, but I'll
> fix all of these once the bug report is complete so I can point to the
> bug report in the SVN commit messages.
>
&
Have you also tried looping over all of the DIFF_MODEL options in one
script, such as:
"""
MODELS_TO_RUN = ['local_tm', 'sphere', 'prolate', 'oblate', 'ellipsoid']
for DIFF_MODEL in MODELS_TO_RUN:
# execute the rest of the full_analysis protocol
# The model-free models (do not ch
I will sync up with the newest CVS version, give it a go, and post
back with the results.
Doug
On Aug 29, 2007, at 10:16 AM, Sebastien Morin wrote:
Hi all,
I just tried, a couple of days ago, the CONV_LOOP = 1 option in the
full_analysis,py script.
Strangely (as opposed to Douglas), it
MF_MODELS with a single test within the model-free
> model loop which already exists - just to simplify the code. The
> changes have been committed to the repository.
>
>
>
>
> On 6/27/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> Another update. I had to chan
S:
>> > if name_to_remove in self.relax.data.run_names:
>> > run.delete(name_to_remove)
>>
>>
>> If you would like me to commit these changes, just let me know where
>> I can find instructions on how to do so.
>>
ts - just to simplify the code. The
> changes have been committed to the repository.
>
>
>
>
> On 6/27/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> Another update. I had to change a few more lines, but the script
>> seems to work properly
07, at 3:58 AM, Edward d'Auvergne wrote:
> Whoops, that should have been 'self.relax.data.run_names'! It's all
> fixed in the repository.
>
> Cheers,
>
> Edward
>
>
> On 6/25/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> Hi Edw
; fixed in the repository.
>
> Cheers,
>
> Edward
>
>
> On 6/25/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
>> Hi Edward,
>>
>> A ne
,
Doug
On Jun 26, 2007, at 3:58 AM, Edward d'Auvergne wrote:
> Whoops, that should have been 'self.relax.data.run_names'! It's all
> fixed in the rep
, at 8:54 AM, Edward d'Auvergne wrote:
> Hi,
>
> Sorry, that relax_data_store was 1.3 line specific and I forgot to
> change that for the 1.2 line. The repository code should now have
> that fixed.
>
> Cheers,
>
> Edward
>
>
> On 6/25/07, Douglas Koje
uvergne wrote:
> Unfortunately my scripts are archived on my personal laptop which I
> don't with me here at work. It may involve using certain relax
> functions (not user functions) located in 'self.relax.generic' or
> 'self.relax.specific'. Most likely you wi
ses
> iteration number, like I did in my thesis in figures 7.3 and 7.4
> (http://eprints.infodiv.unimelb.edu.au/archive/2799/), you'll see
> what is happening there. The plots should help in figuring out
> exactly what is happening.
>
> Regards,
>
> Edward
&g
331052364672359544783831
prolate/round_29: 785.887140331284172134473919868469
prolate/round_30: 785.887140331283262639772146940231
prolate/round_31: 785.887140331282694205583538860083
"""
On Jun 25, 2007, at 3:10 AM, Edward d'Auvergne wrote:
> On 6/25/07, Douglas Kojetin <[E
--end
Thanks,
Doug
On Jun 25, 2007, at 4:42 AM, Edward d'Auvergne wrote:
> Hi,
>
> I've just made modifications to the 1.2 and 1.3 repository lines to
> hopefully fix this problem. Could you try again to see if the script
> works this time?
>
> Cheers,
>
> Edward
&g
;, line 388, in run_script
console.interact(intro, local, script_file, quit)
File "/opt/relax/1.2/prompt/interpreter.py", line 340, in
interact_script
execfile(script_file, local)
File "chisq.py", line 11, in ?
abc=self.relax.data.chi2[name]
KeyError: '
all rounds of optimisation until
> convergence actually works? There could possibly be bugs lurking
> there. Thanks.
>
> The problem that you encountered with the calling of the __init__()
> function is because this function should not be called. Using that
> type of approach, the
said, this scenario is quite unlikely and something
> else is more likely to be the problem. Again a list of the
> chi-squared values for a large number of iterations would be very
> useful in tracking down the issue.
>
> Regards,
>
> Edward
>
>
> On 6/24/07, Douglas
Hi All,
I have two separate but related questions. I am using relax 1.2 (svn
version 3301). I have relaxation data collected at two fields -- 500
and 600 MHz. However, I have data for 9 additional residues at 600
MHz that were unresolved at 500 MHz.
(1) The protein I am studying has two
Hi All,
Is it possible to edit full_analysis.py so the optimization of MII to
MV (self.round > 0) is done automatically by looping until
convergence? I tried to do this by modifying the following in
convergence() [near the end]:
"""
# Final print out.
##
While we are on the topic of model selection/optimization, I am
having some trouble with relax 1.2's full_analysis.py script. I have
optimized the local_tm run, and I ran the initial run on the oblate
tensor (init). When I attempt to optimize the oblate run (round_1),
I see the following
r that you would like to use?
Cheers,
Edward
On 3/28/07, Douglas Kojetin <[EMAIL PROTECTED]> wrote:
Hi All,
Does anyone have an example noe.py script to analyze and average
three identical {1H}-15N NOE experiments?
Thanks,
Doug
___
relax (http
Hi All,
Does anyone have an example noe.py script to analyze and average
three identical {1H}-15N NOE experiments?
Thanks,
Doug
___
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This is the relax-users mailing list
relax-users@gna.org
To unsubscribe from this lis
always significant.
The difference that would concern me is if there are dramatic
differences in order parameters - S2 is generally fairly robust to
the
above issues, within reason.
Cheers,
Chris
On Wed, 2006-12-20 at 16:18 -0500, Douglas Kojetin wrote:
> Hi All,
>
> Has anyone c
difference that would concern me is if there are dramatic
differences in order parameters - S2 is generally fairly robust to the
above issues, within reason.
Cheers,
Chris
On Wed, 2006-12-20 at 16:18 -0500, Douglas Kojetin wrote:
Hi All,
Has anyone compared runs of relax (m1 through m5; full_a
Hi All,
Has anyone compared runs of relax (m1 through m5; full_analysis.py
script) vs. a traditional fastmodelfree/modelfree run using the
binary provided by the Palmer group? I have ... I think I'm using
similar parameters for both runs, and I'm seeing a drastic difference
in results (m
Hi All-
My network connection is extremely slow today, so I am not able to
search the message archives. I am posting this in the hope that
someone knows how to resolve my problem (and I hope the message will
make it out).
I am trying to install relax using the directions in the relax.pdf
Hi Edward-
Do you have a paper on relax in the pipeline to be published soon?
Also, do you have any references to other papers discussing the list
of models found in:
Chapter 10 -- ALPHABETICAL LISTING OF USER FUNCTIONS
10.2.29 model free.select model
(m0-m39, tm0-tm39)
Thanks,
Doug
_
Hello-
I am trying to use the reduced spectral density mapping functionality
in relax. I am using the 'jw_mapping.py' script, provided in the
relax distribution. I see the following error when trying to execute
the run:
relax> value.set(run='jw', value=1.0201e-10,
param='b
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