Re: Question et exemple Relax

mailto:nicolas.dou...@iaf.inrs.ca* *Web: http://www.profs.inrs.ca/ndoucet/* *--* * * -- Sébastien Morin, Ph.D. Postdoctoral Fellow, S. Bernèche Laboratory Department of Bioinformatics Biozentrum, Universität Basel Klingelbergstrasse 50/70 4056 Basel Switzerland sebastien DOT morin AT unibas DOT ch

Re: Question et exemple Relax

: http://www.profs.inrs.ca/ndoucet/* *--* * * -- Sébastien Morin, Ph.D. Postdoctoral Fellow, S. Bernèche Laboratory Department of Bioinformatics Biozentrum, Universität Basel Klingelbergstrasse 50/70 4056 Basel Switzerland sebastien DOT morin AT unibas DOT ch

Re: Temperature calibration T2

-- Sébastien Morin, Ph.D. Postdoctoral Fellow, S. Grzesiek NMR Laboratory Department of Structural Biology Biozentrum, Universität Basel Klingelbergstrasse 70 4056 Basel Switzerland ___ relax (http://nmr-relax.com) This is the relax-users mailing list relax

Re: Relax GUI

/listinfo/relax-users -- Sébastien Morin, Ph.D. Postdoctoral Fellow, S. Grzesiek NMR Laboratory Department of Structural Biology Biozentrum, Universität Basel Klingelbergstrasse 70 4056 Basel Switzerland ___ relax (http://nmr-relax.com) This is the relax

Re: pipe.create() user function

! With dasha.py, even this is not helping. I am sorry if it sounds weird but I am really puzzled as well. Thanks, Shantanu S. Bhattacharyya -- Sébastien Morin, Ph.D. Postdoctoral Fellow, S. Grzesiek NMR Laboratory Department of Structural Biology Biozentrum, Universität Basel Klingelbergstrasse 70

Re: Binding studies

concentration smaller or equal to 1 mM) would yield a steady-state bound population of ~91% (0.91). Cheers, Séb :) On 11-02-24 11:13 AM, Sébastien Morin wrote: Hi, I have not worked with this situation. However, I agree that binding kinetics should be known (on and off rates) and a majority

Gna security issue

. Is this important ? Should this be fixed by the Gna people ? Cheers, Séb :) -- Sébastien Morin, Ph.D. Postdoctoral fellow S. Grzesiek NMR Laboratory Biozentrum, Universität Basel Basel, Switzerland ___ relax (http://nmr-relax.com

Re: Ellipsoid minimization does not converge

list relax-users@gna.org 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-users -- Sébastien Morin PhD Student S. Gagné NMR Laboratory Université Laval PROTEO Québec, Canada

Re: relax on Mac with fink

problem..? Séb On 10-02-22 10:23 AM, Sébastien Morin wrote: Hi Ed, Please see below... On 10-02-22 2:49 AM, Edward d'Auvergne wrote: Hi, See below: On 21 February 2010 20:59, Sébastien Morinsebastien.mori...@ulaval.ca wrote: Hi, I just installed relax on a Mac

Re: relax on Mac with fink

to be performed... Thanks for your insights ! This could be again related to Python versions, with Scientific Python installed for Python 2.6 but relax running with Python 1.5 (Mac Unix software versions are painfully old :P). I hope this helps. Regards, Edward -- Sébastien

Re: Pymol macro script.

information page at https://mail.gna.org/listinfo/relax-users -- Sébastien Morin PhD Student S. Gagné NMR Laboratory Université Laval PROTEO Québec, Canada ___ relax (http://nmr-relax.com) This is the relax-users mailing list relax-users@gna.org

Re: Error when running full_analysis.py script

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-users -- Sébastien Morin PhD Student S. Gagné NMR Laboratory Université Laval PROTEO Québec, Canada

Re: Bug in structure.create diff tensor pdb

Edward d'Auvergne wrote: On Thu, Mar 12, 2009 at 7:04 PM, Sébastien Morin sebastien.mori...@ulaval.ca wrote: Edward d'Auvergne wrote: On Thu, Mar 12, 2009 at 6:05 PM, Sébastien Morin sebastien.mori...@ulaval.ca wrote: Hi, In an attempt to find the problem causing

Re: Bug in structure.create diff tensor pdb

Edward d'Auvergne wrote: On Thu, Mar 12, 2009 at 6:05 PM, Sébastien Morin sebastien.mori...@ulaval.ca wrote: Hi, In an attempt to find the problem causing this bug, I dug into the code and found something which could be erroneous... This alone does not fix the bug, but may be part

Re: Rex value

://nmr-relax.com) This is the relax-users mailing list relax-users@gna.org 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-users -- Sébastien Morin PhD Student S. Gagné NMR

Re: Rex value

Hi, Concerning the AIC value, you're absolutely right. A negligible (- 0) Rex should yield the same chi2 as a nested model, but a AIC value different by 2... Regards, Séb Edward d'Auvergne wrote: On Tue, Mar 10, 2009 at 6:23 PM, Sébastien Morin sebastien.mori...@ulaval.ca wrote: Hi

Bug in structure.create diff tensor pdb

/ relax-1.3.3 and the same problem arises... so the problem as been there for a long time... Shouldn't the tensor always keep a symmetric shape, with angles only changing the orientation, not the shape..? Thanks for help. Séb :) -- Sébastien Morin PhD Student S. Gagné NMR Laboratory Université

Re: X-H vector orientations

as you wish. Regards, Edward On Sat, Jan 17, 2009 at 10:33 PM, Sébastien Morin sebastien.mori...@ulaval.ca wrote: Hi Ed, Thanks for the detailed and rapid answer ! These functionalities would be great ! The use of X-H vectors orientations spread could be used in cases where several

Re: Model-Free Results Output

, that would be very useful. Cheers, Edward On Wed, Oct 22, 2008 at 3:17 AM, Tyler Reddy [EMAIL PROTECTED] wrote: Hi Seb, I just tested 'oblate' and it produces the same error output. Tyler Quoting Sébastien Morin [EMAIL PROTECTED]: Hi Tyler, Do you get the same error

Re: Model-Free Results Output

Oh... Sorry... It's still early in the morning here (Quebec City)... ... Dont' forget to specify a log file... LOG - relax -l LOG script.py TEE - relax -t LOG script.py If you just specify the script, the script will be erased by the log... Cheers, Séb Sébastien Morin wrote: Hi

Re: Model-Free Results Output

Hi Tyler, Do you get the same error when trying the 'oblate' or 'ellipsoid' diffusion tensors ? Sébastien Tyler Reddy wrote: I'm having an issue with the full_analysis.py script. It seems to work fine when DIFF_MODEL = 'local_tm' or 'sphere' (converges on 4th round) but for 'prolate' I

Re: Curve fitting

at 7:02 AM, Chris MacRaild [EMAIL PROTECTED] wrote: On Thu, Oct 16, 2008 at 3:11 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I have a general question about curve fitting within relax. Let's say I proceed to curve fitting for some relaxation rates (exponential decay

Curve fitting

Hi, I have a general question about curve fitting within relax. Let's say I proceed to curve fitting for some relaxation rates (exponential decay) and that I have a duplicate delay for error estimation. delays 0.01 0.01 0.02 0.04 ... Will the mean value (for delay 0.01) be

Re: Full analysis issue

of the protein released? What is the system which is being studied? What are the AIC values like for each global model? Anyway, hopefully one of these ideas may be of help in sorting out the problem. Regards, Edward On Mon, May 5, 2008 at 9:23 PM, Sébastien Morin [EMAIL PROTECTED] wrote

Re: Error message with the script palmer.py

floating point numbers in the mfout file is dangerous. The algorithm should handle column fusions anywhere in the mfout file where 2 floating point numbers are located side by side. I'll have to think about this one some more. Cheers, Edward On Tue, Apr 8, 2008 at 5:19 PM, Sébastien Morin

Re: Hybrid model and writing of results

be many diffusion tensors for different spins, or no diffusion tenor for some spins)). This code will not make it to the 1.2 relax versions though. Regards, Edward On Fri, Apr 4, 2008 at 10:14 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I encountered an error with the results.write

Re: Hybrid model and writing of results

, Apr 9, 2008 at 3:17 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi Ed, I understand. However, I would like to know if it is possible to calculate the AIC for a given hybrid... and possibly compare different hybrids together within relax... Thanks ! Have a nice day ! Séb

Error message with the script palmer.py

Hi, I am using the script palmer.py to extract dynamic information using AIC model selection, but ModelFree4 as an optimization tool. I tried the script several times before with a good success, however, I now get an error message when trying to extract parameters for model m5 during stage 2.

Re: Constraints in full_analysis.py

then release a new version of relax. Could you make a bug report for this? Cheers, Edward On Mon, Apr 7, 2008 at 9:40 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I am using the full_analysis.py script and got an intriguing warning in the final step. It seems there is a problem

Re: AIC from ModeFree data

... For the run 'None' being selected, yes, it is for all spins... Running with the '--debug' flag doesn't change anything... Cheers, Séb Edward d'Auvergne wrote: On Wed, Apr 2, 2008 at 7:11 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I tried to use the palmer.extract() function

Re: AIC from ModeFree data

. Regards, Edward On Tue, Apr 1, 2008 at 11:41 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I have different model-free analysis that originated from the program ModelFree (with results in a 'mfout' file). I would like to know if there is a way of loading these data to proceed to model

Re: AIC from ModeFree data

. Regards, Edward On Tue, Apr 1, 2008 at 11:41 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I have different model-free analysis that originated from the program ModelFree (with results in a 'mfout' file). I would like to know if there is a way of loading these data to proceed to model

AIC from ModeFree data

Hi, I have different model-free analysis that originated from the program ModelFree (with results in a 'mfout' file). I would like to know if there is a way of loading these data to proceed to model selection by AIC using relax. I there ain't any way of doing this, I'll turn to the palmer.py

Re: Spectral Density Mapping Problem

Hi Johnny ! I would be helpful if you could post, let's say, the first 10 lines of each input file as well as the complete script you used. Moreover, it could be also useful to know which version of relax you use... Cheers ! Séb :) Johnny Croy wrote: Hello, I am new to using relax,

Re: Lagrange multiplier warning

: On Fri, Feb 22, 2008 at 6:03 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I am trying to use the full_analysis.py script for optimizing model m11 to m15 (m1 to m5 with CSA) for a system for which I have datasets at three magnetic fields (500, 600, 800 MHz). The optimization is quite long

Re: Spectral Density Mapping Problem

with your own files ? Let me know if it works now... Cheers ! Sébastien :) Johnny Croy wrote: Duh...my bad. On Mar 25, 2008, at 11:18 AM, Sébastien Morin wrote: Hi Johnny This is a private message (out of the mailing list). To get everything saved in the mailing list archive, please

Re: Constraints

of linear_constraints(). I hope this info helps. Regards, Edward On Fri, Feb 22, 2008 at 5:38 PM, Sébastien Morin [EMAIL PROTECTED] wrote: Hi, I have a question about constraints in relax... I would like to know what are the built-in constraints in relax, especially for what concerns 'tau

Re: Spectral Density Mapping Problem

, Sébastien Morin [EMAIL PROTECTED] wrote: Hi Johnny ! I put all you data in the correct files on my laptop (names as in the script) and everything seems to work fine... I am using the 1.2 line, revision 5232 (subversion repository)... Please try to run the script with the attached files

Constraints

Hi, I have a question about constraints in relax... I would like to know what are the built-in constraints in relax, especially for what concerns 'tau' (tau_m, tau_e, tau_s, tau_f) as well as 'r' and 'csa' (for models m1x and m2x). What I'd like to know is if those parameters are contrained

Lagrange multiplier warning

Hi, I am trying to use the full_analysis.py script for optimizing model m11 to m15 (m1 to m5 with CSA) for a system for which I have datasets at three magnetic fields (500, 600, 800 MHz). The optimization is quite long, but this could be due to the algorithm used. I'll thus try to optimize

Re: looping the optimization in full_analysis.py

||| || || |___| __ Sébastien Morin Étudiant M.Sc. Biochimie Laboratoire S. Gagné 3252 Pav. Marchand