Proline residues in 3D structures

a really important issue. However, the PDB loading function could be modified slightly to avoid it looking for atoms that can't exist... What do you think of this idea ? Séb -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP

Error in the manual

tensor(‘m8’, (8.5e-9, 1.1, 20.0, 20.0), param types=1) = The param_types should be 2. Cheers, Séb -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656

Re: Error in the manual

. Would you like to make the fix to the 1.3 line and then use svnmerge to port the revision to the 1.2 line? I'm just updating the svnmerge status of the 1.2 line now. Thanks, Edward On Feb 8, 2008 5:20 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I found an error in the manual

Re: [bug #11004] Model elimination

___ Reply to this item at: http://gna.org/bugs/?11004 ___ Message sent via/by Gna! http://gna.org/ -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique

Re: r4821 - /1.3/maths_fns/jw_mapping.py

-- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 ___ relax (http://nmr-relax.com) This is the relax-devel mailing list relax

Re: Running individual tests

as well, then individual tests can be run. But for now, the most you can do to narrow it down is to type: relax --system-tests Regards, Edward On Jan 11, 2008 6:40 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I would like to run individual tests (e.g. run only the system test

Re: r4647 - /branches/consistency_tests_1.3/

://mail.gna.org/listinfo/relax-commits -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530 ___ relax (http://nmr

Re: r4654 - /branches/consistency_tests_1.3/generic_fns/selection.py

into your branch. Note that these changes have gone into the 1.3 line and not your branch first. This is very important. Regards, Edward On Jan 11, 2008 9:25 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, Cool ! :p I'll wait for you to find out how the circular problem can be solved

Re: r4654 - /branches/consistency_tests_1.3/generic_fns/selection.py

= ___ relax (http://nmr-relax.com) This is the relax-commits mailing list [EMAIL PROTECTED] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits -- Sebastien Morin

Re: r4654 - /branches/consistency_tests_1.3/generic_fns/selection.py

that revision to get the import back (reverting the reversion). But the problem is a circular import issue. I'll look into what is causing this and hopefully have the answer today. This can be a difficult problem to solve in a large program. Regards, Edward On Jan 11, 2008 9:07 PM, Sebastien Morin

Re: r4526 - /1.3/test_suite/unit_tests/_prompt/test_minimisation.py

-relax.com) This is the relax-commits mailing list [EMAIL PROTECTED] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits -- Sebastien Morin Etudiant au PhD en biochimie

Re: r4526 - /1.3/test_suite/unit_tests/_prompt/test_minimisation.py

for making the changes. Regards, Edward On Jan 9, 2008 6:13 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Also... Do we need to keep the print_flag argument for all minimise() calls or only for generic_minimise() calls ? Cheers Séb Sebastien Morin wrote: Hi, If we have

Re: r4526 - /1.3/test_suite/unit_tests/_prompt/test_minimisation.py

all calls to generic_minimise() should keep the print_flag keyword argument for now (so 'print_flag=print_flag' becomes 'print_flag=verbosity'). I will probably change the print_flag arg in the minfx project as well, but not right now. Cheers, Edward On Jan 9, 2008 5:28 PM, Sebastien Morin [EMAIL

Re: Shifting the consistency testing code to the new relax design.

together with relax. Regards, Edward On Tue, 2008-01-08 at 13:31 -0500, Sebastien Morin wrote: Hi, Could you tell me what will be the change so I can try to make it for the consistency_test code and, if good, port it to the jw_mapping code ? Maybe some old posts in the mailing lists talked

Re: r4466 - /branches/consistency_tests_1.3/maths_fns/consistency_tests.py

is the diff : # Copyright (C) 2007-2008 Sebastien Morin # --- # Copyright (C) 2007 Sebastien Morin # 25c25 from math import pi --- from math import pi, cos

Re: r4266 - /1.3/test_suite/unit_tests/value_testing_base.py

PROTECTED] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane

Re: r4514 - /branches/consistency_tests_1.3/test_suite/unit_tests/value_testing_base.py

-relax.com) This is the relax-commits mailing list [EMAIL PROTECTED] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits -- Sebastien Morin Etudiant au PhD en biochimie

Re: r4211 - /branches/consistency_tests_1.3/sample_scripts/consistency_tests.py

for reduced spectral density mapping. +# Script for consistency testing. # Create the run. -name = 'jw' -run.create(name, 'jw') +name = 'consistency' +run.create(name, 'ct') This user function is now called pipe.create(). Others may change later. Regards, Edward -- Sebastien

Re: r4200 - in /1.2: generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/

: That is a strange problem. Maybe it would be best to get clean, fresh versions of all the relax SVN code. You have registered SSH public keys with Gna! for all the machines you are using? Regards, Edward On Dec 18, 2007 3:45 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I

Re: r4214 - /branches/consistency_tests_1.3/specific_fns/consistency_tests.py

://nmr-relax.com) This is the relax-commits mailing list [EMAIL PROTECTED] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits -- Sebastien Morin Etudiant au

Re: r4200 - in /1.2: generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/

to delete the 1.2 checked out copy you have and check it out again. Maybe there is a corruption somewhere in that copy? Regards, Edward On Dec 18, 2007 2:40 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi Ed, As you proposed, I checked out a new fresh copy of the main 1.2 line

Re: r4200 - in /1.2: generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/

revert revisions 4204 and 4202 (the undeleting of the branch) ? Don't you get this message when trying the same command from a fresh copy (r4204) of the main 1.2 line ? Cheers Séb Edward d'Auvergne wrote: On Dec 18, 2007 5:04 AM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi again

Re: Integration of the consistency_tests branch (and becoming a relax committer).

if this helps, otherwise I'll search for another solution. Regards, Edward On Dec 14, 2007 8:57 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi again I forgot to specify my svn version and system so that my problem with the 'svn ci -F svnmerge-commit-message.txt' command may

Re: Integration of the consistency_tests branch (and becoming a relax committer).

the changes that happened in the 1.3 line to the branch before starting the work (However, svnmerge does not seem to have been initialized in this branch right now.) ? Cheers Séb :) Edward d'Auvergne wrote: On Dec 17, 2007 7:52 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi Ed, You were

Re: r4200 - in /1.2: generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/

-relax.com) This is the relax-commits mailing list [EMAIL PROTECTED] To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits -- Sebastien Morin Etudiant au PhD en

Re: r4200 - in /1.2: generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/

is revertable in SVN, even is someone decided to delete every last file in the repository. Regards, Edward On Dec 17, 2007 11:52 PM, Sebastien Morin [EMAIL PROTECTED] wrote: Hi Ed, The last number was 3532 since no change has occured in the branch since this revision... Also, the merges were

Re: Integration of the consistency_tests branch (and becoming a relax committer).

/tools_contrib.html#svnmerge_py Cheers Séb :) Sebastien Morin wrote: Hi Ed, Ok, this svnmerge.py tool seems great ! Here's what I tried : 1. Move to the consistency-tests branch (line 1.2) directory (on my laptop). 2. svnmerge.py avail 3. svnmerge.py merge -r3343,3347-3349,3353-3354,3356

Re: Integration of the consistency_tests branch (and becoming a relax committer).

://[EMAIL PROTECTED]/svn/relax/branches/consistency_tests_1.2 Is that what I should do, do I miss some steps or am I completely wrong..? Thanks ! Sébastien :) Sebastien Morin wrote: Hi Ed ! I think the consistency tests code is ready for integration into the main 1.2 line. I am now

Re: Integration of the consistency_tests branch (and becoming a relax committer).

, I use it to back-port bug fixes from the 1.3 line to the 1.2 line. For branches, all of the changes which occurred to the line the branch originates from must be merged. Regards, Edward -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr

Re: Precision in the test-suite

, Edward On 10/22/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi again... Here are two patches if the changes I proposed for the precision in the jw_mapping and consistency tests test-suites were to be accepted as relevant... 1. patch_precision_in_test-suite_1.2-r3370_jw_mapping

Re: Reduced spectral density mapping at three fields

automatically... Cheers Sébastien :) Edward d'Auvergne wrote: On 10/16/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi Daniel Calculations for the reduced spectral density mapping need only the R1, R2 and NOE at one field. R1, R2 and NOE are 3 variables you measure and you extract 3

Re: Command name as seen with 'top'

argv[0] this will change the name of you application) However, they appear to be horribly messy in all the versions i have seen so far (cf http://davyd.livejournal.com/166352.html) regards gary On 9/2/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I would like to know

Command name as seen with 'top'

if this kind of modification is hard to make for the relax code... I'm just asking in case it's an easy task... Thanks ! Séb :) -- __ ___ | | || Sebastien

Re: Data set format

would you use? The system has to be flexible enough to handle absolutely all rubbish thrown at it by a user ;) Cheers, Edward On 8/21/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi all ! I am now analysing data using relax (line 1.2, branch consistency-tests, revision 3354). I

Re: Data set format

would you use? The system has to be flexible enough to handle absolutely all rubbish thrown at it by a user ;) Cheers, Edward On 8/21/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi all ! I am now analysing data using relax (line 1.2, branch consistency-tests, revision 3354). I

Data set format

for the duplicate request... Cheers ! Sébastien :) -- __ ___ | | || Sebastien Morin || ||| Etudiant au PhD en biochimie

Re: Consistency tests

, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, When I adapted the jw_mapping code to yield the consistency_test code, I didn't understand why, in the test suite, the following lines : if abs(self.relax.data.res[self.run][index].j0 - j0[index]) j0[index]/1e6: print

Re: Consistency tests

stable. Cheers, Edward On 6/26/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I started working on implementing the consistency tests last week before the last post was made and, hence, I worked on repository line 1.2 (revision 3303). I implemented the consistency tests

Re: Consistency tests

Hi again and again Here is a third patch for the code 'test-suite/consistency_tests.py' of the 1.2 branch for consistency testing. Cheers Séb Index: test_suite/consistency_tests.py === --- test_suite/consistency_tests.py

Re: Consistency tests

) 2007 Sebastien Morin sebastien.morin.1 at ulaval.ca' underneath the already existent copyright text. The can be changed later, for example I can give you a [EMAIL PROTECTED] email address which is an alias for any other email address (once voted in as a relax developer). Could you add

Re: Consistency tests

Hi Here the patch for the file 'maths_fns/consistency.py' Séb :) Sebastien Morin wrote: Hi again ! Here is again the first patch for the file 'prompt/consistency_tests.py'. I modified the header for the copyrights. Also, the former patches were not copied-pasted, but attached using

Re: Consistency tests

Hi again Here the patch for 'test_suite/consistency_tests.py'. Bye Séb Sebastien Morin wrote: Hi, Here is the patch for the file 'specific_fns/consistency_tests.py'. Ciao ! Sébastien Sebastien Morin wrote: Hi Here the patch for the file 'maths_fns/consistency.py' Séb

Re: Consistency tests

that, for the record, the files are located within the permanent relax infrastructure. Cheers, Edward On 7/9/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi again ! Here is again the first patch for the file 'prompt/consistency_tests.py'. I modified the header

Re: Formating issues in the 1.3 line

options, visit the list information page at https://mail.gna.org/listinfo/relax-devel -- __ ___ | | || Sebastien Morin

repository line 1.3

Hi, I just checked out the repository line 1.3 and tried the test suite without success. Should the 1.3 line work or is it supposed to crash on almost every single test..? Please find below the error output (first 120 lines) from the test suite. You'll see that the error is always something

Re: repository line 1.3

of the program. Regards, Edward On 6/27/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I just checked out the repository line 1.3 and tried the test suite without success. Should the 1.3 line work or is it supposed to crash on almost every single test..? Please find below the error output

Re: Consistency tests

it will need to be added to the 1.3 line for it to exist within future relax versions. Thank you for this great effort. Cheers, Edward On 6/26/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I started working on implementing the consistency tests last week before the last post was made

Re: Consistency tests

been playing with? Cheers, Edward On 6/15/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi everyone During the last months, I was astonished to realize that some spin relaxation data I had acquired at different fields were not consistent between each other. The way I realized

Re: [bug #9259] Reduced spectral density mapping yielding bad values

is not designed to handle large attachments. On 6/19/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi, I agree quite well with what you say. However, I would have thought that, even if radians are often implied and not discussed, they should be present in the IUPAC reports (see attached file

Re: [bug #9259] Reduced spectral density mapping yielding bad values

the value in self.data.frq_list[0, 1], the frequency of the heteronucleus, to calculate the CSA constant. The higher frequencies are never used in the calculation. Anyway, your patch fixes this problem. On 6/13/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi ! I've checked the equations

[bug #9259] Reduced spectral density mapping yielding bad values

Hi, Sorry about that, but I forgot to tell for which version and revision the patch is for... repository 1.2 revision 3301 Seb ___ relax (http://nmr-relax.com) This is the relax-devel mailing list relax-devel@gna.org To unsubscribe from this list,

Re: [bug #9259] Reduced spectral density mapping yielding bad values

subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-devel -- __ ___ | | || Sebastien Morin

Re: Join the team

/07, Sebastien Morin [EMAIL PROTECTED] wrote: Hi everyone Some weeks ago, after one question of mine on reduced spectral density mapping, Edward proposed that someone could add the multiple field J(0) optimization feature to relax in order to improve the jw mapping option. I could

Join the team

Hi everyone Some weeks ago, after one question of mine on reduced spectral density mapping, Edward proposed that someone could add the multiple field J(0) optimization feature to relax in order to improve the jw mapping option. I could be interested in that task... However, I must confess I am

Re: Representing the Brownian rotational diffusion tensor in Molmol, etc.

/06, Sebastien Morin [EMAIL PROTECTED] wrote: Hi all ! I also like the Tensor representation of the diffusion tensor. If Molmol is a problem for connectivities and heteroatoms, why not change relax to output script for Pymol instead of Molmol ? This is just a proposition since I'm a Pymol

Re: Representing the Brownian rotational diffusion tensor in Molmol, etc.

-- __ ___ | | || Sebastien Morin || ||| Etudiant au PhD en biochimie ||| Laboratoire de resonance magnetique nucleaire | Dr Stephane Gagne