Re: 13C relaxation Model-free

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 >

Re: S^2 differences between proteins

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

Re: Relax app MacOS run script

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

Re: Relax app MacOS run script

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. >

Re: Error in model free analysis

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,

Re: Error in setting up model free analysis

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",

Re: Error in setting up model free analysis

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

Re: Dispersion Back Calculation

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

Re: Dispersion Back Calculation

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

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

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

Re: Using modified all models free

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

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

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

Re: Using multi-processor for model_free

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

Re: Dispersion Back Calculation

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 >

Re: Using multi-processor for model_free

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

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

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

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

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

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

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

Re: Using multi-processor for model_free

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

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

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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',

Re: Using multi-processor for model_free

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

Re: Issue in ModelFree Calculation

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

Re: Using multi-processor for model_free

On 30 September 2016 at 01:35, Mahdi, Sam wrote: > Also, Congrats to Edward! Thanks :) ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a

Re: Using multi-processor for model_free

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:

Re: Using multi-processor for model_free

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.

Re: Using multi-processor for nmr relax

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"

Re: Using multi-processor for nmr relax

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

Re: Troubleshooting model-free analysis

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

Re: error in final execution of NOE in relax

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 >

Re: Troubleshooting model-free analysis

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

Re: Issue in ModelFree Calculation

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

Re: missing data in relaxation dispersion

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 p

Re: missing data in relaxation dispersion

, 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 Padr

Re: Data files

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

Re: missing data in relaxation dispersion

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,

Re: regarding installation

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,

Wiki spam bot cleanup.

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

Re: How to make one fit from two experiments.

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

Re: Experimental: Try relax at Google Cloud Computing

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

Re: model free analysis: spin deselection problem

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,

Re: model free analysis: spin deselection problem

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

Re: back calculation of relaxation data

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 r

Re: back calculation of relaxation data

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: >

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

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

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

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 , &g

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

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

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

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 >

Re: Model free on symmetric homodimer, problems with grace plots

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

Re: fixed tm values

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

Re: using relax on supercomputer

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

Re: Problems Loading PDB

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

Re: using relax on supercomputer

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

Re: Problems Loading PDB

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

Re: Help with setting up relax files

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

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

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

Re: Error calculation of individual parameter dw from MC

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

Re: Error calculation of individual parameter dw from MC

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

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

Re: error on the diffusion tensor parameters

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,

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

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

Re: error while running relax-GUI tutorial

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

Re: error while running relax-GUI tutorial

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

Re: C modules not compiled

) 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

Re: C modules not compiled

). 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

Re: Reg : Input files for model free analysis

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

Re: Regarding Relax-3.3.0 NMR installation

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,

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

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).

Re: Relaxation dispersion clustering calculation time

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

Re: Relaxation dispersion clustering calculation time

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

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

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

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

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

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

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 d'Auvergne edw...@nmr-relax.com wrote: Hi Atul, Again continuing from Troels' post at http

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

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.

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

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

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

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

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

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

Re: dimer

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

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

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

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

. 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

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

, 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

Re: R1rho RD analysis

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

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

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

Re: Side chain dynamics

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

Re: R1rho RD analysis

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

Re: R1rho RD analysis

. 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

Re: R1rho RD analysis

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

Re: dimer

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

Re: dimer

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

Re: dimer

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

Re: dimer

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

Re:

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

Re: Re:

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

Re: Re:

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

The hidden radian unit in relaxation dispersion.

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

Re: Model-free analysis error

% 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

Re: Model-free analysis error

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

Re: Model-free analysis error

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

Re: Processing again

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

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