relax (molecular dynamics analysis)

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 ... [More] 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 disp [Less]

Hi Prem, Welcome to the relax mailing lists! For the problem you are seeing, could you please create a bug report for this (https://gna.org/bugs/?func=additem&group=relax)? Cheers! It would be good to know what steps you took to encounter ... [More] this bug, and where in the analysis the problem occurred. The more details you give, the easier it will be for me to reproduce the problem. Once a relax developer can reproduce a bug (via a system test), then a solution often only takes 5 to 10 minutes to implement. The best would be to attach data to the bug report - in this case a relax save state just prior to the bug occurring. Could you also include the output of the 'relax --info' command? Cheers, Edward On 18 November 2014 00:06, Prem Raj Joseph <prbj123relax-Re5JQEeQqe8AvxtiuMwx3w< at >public.gmane.org> wrote: [Less]

Hello all, I was using the GUI version of the software to run the tutorial available in the manual for analysis of relaxation dispersion. When i execute the run I get the following error RelaxPipeError: RelaxError: The data pipe 'R2eff - relax_disp ... [More] (Mon Nov 17 10:50:08 2014)' already exists. Not sure where the error is arising from. Any help is greatly appreciated. Thanks Prem Department of Biochemistry and Molecular Biology Sealy Center for Structural Biology and Molecular Biophysics 5.142 Medical Branch Building University of Texas Medical Branch Galveston, TX 77555-1055 Lab: 409-772-2181 Cell: 409-354-8536 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Error analysis ============== Skipping the error analysis as it has already been performed. relax> relax_disp.r1_fit(fit=False) --------------------- - The 'R2eff' model - --------------------- relax> pipe.copy(pipe_from='origin - relax_disp (Mon Nov 17 10:50:08 2014)', pipe_to='R2eff - relax_disp (Mon Nov 17 10:50:08 2014 [Less]

Update of bug #22963 (project relax): Status: None => Invalid Open/Closed: Open => Closed ... [More] _______________________________________________________ Follow-up Comment #4: The problem in this case was the PDB file test_suite/shared_data/model_free/sphere/sphere.pdb. It has no CONECT records and all the nitrogens are at [0, 0, 0]: ATOM 1 N GLY 1 0.000 0.000 0.000 1.00 0.00 ATOM 2 H GLY 1 0.745 0.000 -0.667 1.00 0.00 ATOM 3 N GLY 2 0.000 0.000 0.000 1.00 0.00 ATOM 4 H GLY 2 -0.373 0.645 -0.667 1.00 0.00 ATOM 5 N GLY 3 0.000 0.000 0.000 1.00 0.00 ATOM 6 H GLY 3 -0.373 -0.645 -0.667 1.00 0.00 ATOM 7 N GLY 4 0.000 0.000 0.000 1.00 0.00 ATOM 8 H GLY 4 1.000 0.000 0.000 1.00 0.00 ATOM 9 N GLY 5 0.000 0.000 [Less]

URL: <http://gna.org/bugs/?22963> Summary: Using '< at >N*' to define the interatomic interactions for a model-free analysis fails when using non-backbone 15N spins. Project: relax ... [More] Submitted by: bugman Submitted on: Mon 17 Nov 2014 10:08:56 AM UTC Category: relax's source code Specific analysis category: Model-free analysis Priority: 5 - Normal Severity: 3 - Normal Status: None Assigned to: bugman Originator Name: Originator Email: Open/Closed: Open Release: 3.3.2 Discussion Lock: Any Operating System: All systems _______________________________________________________ Details: During the dauvergne_protocol model-free auto-analysis, the error seen is: """ Traceback (most recent call last): File "/data/relax/relax-trunk/test_suite/system_tests/model_free.py", line 810, in test_dauvergne_protocol_sphere [Less]

Update of bug #22961 (project relax): Status: None => Fixed Open/Closed: Open => Closed ... [More] _______________________________________________________ Reply to this item at: <http://gna.org/bugs/?22961> _______________________________________________ Message sent via/by Gna! http://gna.org/ [Less]

URL: <http://gna.org/bugs/?22961> Summary: Loading of relaxation data fails with "IndexError: list index out of range". Project: relax Submitted by: bugman Submitted on: Mon 17 Nov ... [More] 2014 07:55:51 AM UTC Category: relax's source code Specific analysis category: Model-free analysis Priority: 5 - Normal Severity: 3 - Normal Status: None Assigned to: bugman Originator Name: Originator Email: Open/Closed: Open Release: 3.3.2 Discussion Lock: Any Operating System: All systems _______________________________________________________ Details: The loading of relaxation data, in some rare cases, fails with and IndexError. This is now caught by the Mf.test_data_loading_failures system test: ====================================================================== ERROR: test_data_loading_failures (test_suite.syst [Less]

This is a minor feature and bugfix release. It includes improvements to the readability of the HTML version of the manual (http://www.nmr-relax.com/manual/index.html), improved printouts throughout the program, numerous GUI enhancements, and far ... [More] greater Python 3 support. Please see below for a full listing of all the new features and bugfixes. For the official, easy to navigate release notes, please see http://wiki.nmr-relax.com/Relax_3.3.2. The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html). The full list of changes is: Features: * Many improvements for the HTML version of the manual at http://www.nmr-relax.com/manual/index.html. * Improved sectioning printouts in the model [Less]

Troels and Edward, Thanks for your assistance. Everything is working fine now. I was using the source code to install (relax-3.3.2.src) and the relax_fit.so file was not present causing the problem. From the base directory I typed "scons", which ... [More] created the relax_fit.so file, and then "scons install " to install the program in /usr/local/relax and create the byte-compiled *.pyc files and everything was fine. I did not realize that I needed to perform the "scons" command first before the "scons install" command. I also downloaded the pre-build relax-3.3.2.GNU-Linux.x86_64 package and it ran fine as well. Thanks again, Mark -----Original Message----- From: edward.dauvergne< at >gmail.com [mailto:edward.dauvergne< at >gmail.com] On Behalf Of Edward d'Auvergne Sent: Friday, November 14, 2014 4:20 AM To: Troels Emtekær Linnet Cc: Maciejewski,Mark W.; relax-users< at >gna.org Subject: Re: C modules not compiled Hi Mark, Welcome to the relax mailing lists! The problem you see could be due to a num [Less]

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 ... [More] 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 <edward< at >nmr-relax.com> wrote: ________________________________ [Less]