CSA & bond length

stien -- __ ___ | | || Sebastien Morin || ||| Etudiant au doctorat en biochimie ||| Laboratoire de resonance magnetique nucleaire | Dr Stephane Gagne | CREFSIP (Universite

Re: CSA & bond length

on options, visit the list information page at https://mail.gna.org/listinfo/relax-users -- __ ___ | | || Sebastien Morin || ||| Etudiant au doctorat en biochimie ||| Laboratoire de resonance magnetique nucleaire |

Re: CSA & bond length

yet. > > Edward > > > P.S. I might change the sample scripts to -170 ppm. I had intended > to change the value a while back but forgot about it. > > > > On 9/30/06, Sebastien Morin <[EMAIL PROTECTED]> wrote: >> >> Hi again >> >> T

Diffusion Tensor - Global correlation time

-- __ ___ | | || Sebastien Morin || ||| Etudiant au doctorat en biochimie ||| Laboratoire de resonance magnetique nucleaire | Dr Stephane Gagne | CREFSIP (Universite Laval

Re: Diffusion Tensor - Global correlation time

. A., and Bax, A. (1989) Biochem. 28(23), > 8972-8979. > Orekhov, V. Y., Korzhnev, D. M., Diercks, T., Kessler, H., and > Arseniev, A. S. (1999a) J. Biomol. NMR 14(4), 345-356. > Orekhov, V. Y., Korzhnev, D. M., Pervushin, K. V., Hoffmann, E., and > Arseniev, A. S. (1999b) J. Biomo

full_analysis.py

Hi ! I am trying the script full_analysis.py with my data. I work with data at three different magnetic fields for 220 residues on a 271 residue protein. I successfully ran the script with the local_tm model, and then with all other diffusion models (sphere, prolate, oblate and ellipsoid) as wha

Re: full_analysis.py

Hi The simplest diffusion model ended the first round after 42h00 on a Intel Pentium4 3.20GHz (Pelican)... Now, after more than 50h00, the oblate (Intel Xeon CPU 2.80GHz, Hibou 1st CPU), prolate (Intel Xeon CPU 2.80GHz, Hibou 2nd CPU) and ellipsoid (Intel Pentium4 CPU 3.20GHz, Pigeon) diffusion m

Re: full_analysis.py

Hi all ! Thanks for sending me your comments and feelings... Here is an update of my benchmarks. Times are not precise though... only approximations based on a rapid lookup of the time stamps for my log files and outputs. All machine are x86 from Dell and run under Gentoo Linux (http://www.gento

Re: full_analysis.py

Hi ! For my model-free analysis, it finally converged. However, when I first tried the final optimization, it didn't work because of bug 7616 (I think)... I'm about to try that final optimization again since I had to work on other things for the last few weeks... In summary, it took, for my 271

Reduced spectral density mapping

Hi everyone ! I just started using the jw_mapping.py script to get spectral densities out of my data. I have some questions : 1. Reading about reduced spectral density mapping, I thought one would extract J(0), J(wN) and J(0.87wH). However, when reading the results file from the jw_mapping.py sc

Test-suite

for helping me solve this obviously easy issue... Sébastien :) -- __ ___ | | || Sebastien Morin || ||| Etu

Re: Reduced spectral density mapping

:) Edward d'Auvergne wrote: > On 11/29/06, Sebastien Morin <[EMAIL PROTECTED]> wrote: >> Hi everyone ! >> >> I just started using the jw_mapping.py script to get spectral densities >> out of my data. >> >> I have some questions : >> >> 1. &g

Convergence on different systems

Hi I used the full_analysis.py script until convergence for the 4 diffusion models (sphere, prolate, oblate, ellipsoid), each on one different computer. Those computer, however, are quite similar, all 32-bits x86 Gentoo Linux with same kernel, gcc, python, etc. For the final run, I switched on a

Reduced spectral density mapping VS Rex

timescale motions) from my data using reduced spectral density mapping at those three fields ? Thanks !! Sébastien :) -- __ ___ | | || Sebastien

Stop and restart

Hi everyone We just had a major electricity failure in Quebec City and Laval University campus and this incident raised questions. I wonder if it is possible to stop a relax run and then restart it exactly where it was. I know it is possible with some programs... If it is not possible, I guess I

Re: {1H}-15N NOE analysis

m) >> >> >> >> 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 p

Re: {1H}-15N NOE analysis

lax-users/2007-03/msg5.html). This > will allow for backwards compatibility with relax scripts. Seb, do > you see this approach as being sufficient? > > Cheers, > > Edward > > > On 3/30/07, Sebastien Morin <[EMAIL PROTECTED]> wrote: >> Hi all >&

Re: CSA & bond length

oteins >> > is highly variable. >> > >> > Idealy for highly accurate model-free analysis, the CSA value should >> > be determined either prior to or during model-free analysis using one >> > of his techniques. However most people appear happy

Re: CSA & bond length

inearity with NH bond, symmetric CSA tensor). > > Alex Hansen > > > On 7/16/07, *Sebastien Morin* <[EMAIL PROTECTED] > <mailto:[EMAIL PROTECTED]>> wrote: > > Hi, > > It's been a long time since we discussed this (the CSA / bond length > issue

NOE errors

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

Re: looping the optimization in full_analysis.py

t;>>>>>> full_analysis.py script in the relax repository (to both >>>>>>>>>> >>>>> the 1.2 >>>>> >>>>>>>>> and >>>>>>>>>

PDB orientation

model-free analysis using ModelFree). Thanks ! Sébastien :) -- __ ___ | | || Sebastien Morin || ||| Etudiant au

Error propagation for duplicates, triplicates, quadriplicates...

so, in the case of duplicates or triplicates, should one use the same approcah ? Thanks ! Séb :) -- __ ___ | | || Sebas

Extremely long optimization times

would, on the contrary, speed up calculations... Thanks for ideas ! Sébastien :) -- __ ___ | | || Sebast

Re: Extremely long optimization times

ithm first and then complete to > high precision with the Newton algorithm. In this case I would use > simplex first followed by the default Newton algorithm and its default > subalgorithms. In all cases constraints should be used. This will > only solve the long computation times if t

Re: Reduced spectral density mapping at three fields

--------- >> >> Message: 1 >> Date: Sun, 3 Dec 2006 01:50:45 +1100 >> From: "Edward d'Auvergne" <[EMAIL PROTECTED]> >> Subject: Re: Reduced spectral density mapping >> To: "Sebastien Morin"

Re: looping the optimization in full_analysis.py

and of the approaches used for calculation/optimization... > > would be extremely useful. > > Doug > > > > On Oct 22, 2007, at 4:15 PM, Sebastien Morin wrote: > >> Hi all ! >> >> First of all, I think that the new feature for automatic looping is >> qui

Re: Reduced spectral density mapping at three fields

rtosis coefficients calculated also 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 >&

Re: looping the optimization in full_analysis.py

analysis.py > script to automatically loop through local_tm, sphere, prolate, oblate > and ellipsoid runs as well. This, however, produces one extremely > large output file, so the modifications mentioned below would be useful. > > Doug > > On Oct 22, 2007, at 4:22 PM, Sebastien Morin

Re: looping the optimization in full_analysis.py

nd run the other tensor runs. > > Doug > > On Oct 24, 2007, at 8:25 AM, Sebastien Morin wrote: > >> Hi Doug >> >> This extreme looping should be added as an option in the >> full_analysis.py script. I'm not sure I would routinely use it as the >> computi

Re: Extremely long optimization times

Hi Ed I didn't have time to try your tips, but they should help me out when I try to run the full_analysis.py script again... I'll let you know if it works well or if I still get long computation times... Cheers Séb :) Edward d'Auvergne wrote: > Hi, > > On 9/17/07,

Re: PDB orientation

in the different structures > are different. > > Regards, > > Edward > > > > On 8/30/07, Sebastien Morin <[EMAIL PROTECTED]> wrote: > >> Hi, >> >> I am doing different tests with the full_analysis.py script, data at >> three magnetic fi

Re: Reduced spectral density mapping at three fields

(https://mail.gna.org/public/relax-devel/2007-10/msg6.html) are now replaced by modified patches made on revision 3375 of line 1.2. Here are the commit messages for the attached patches. === Application of a patch by Sebastien Morin (sebastien dot

Re: PDB orientation

d the lack of theory addressing this > - this really is not an issue for the faint hearted! > > Regards, > > Edward > > > On 10/24/07, Sebastien Morin <[EMAIL PROTECTED]> wrote: > >> Hi Ed >> >> Thanks for the information about the relative

Problem with the palmer.py script

Hi all, I got an error while using the palmer.py script with the 1.2 line of relax (subversion repository). The data was recorded at only one field for a protein with no 3D structure. I first tried to run the three stages one after the other (1, 2, 3) with no monte carlo simulations (sims=0).

Re: Problem with the palmer.py script

Hi again, I found out that my problem had been proposed as a bug some months ago... This is bug 8997. Cheers Séb Sebastien Morin wrote: > Hi all, > > I got an error while using the palmer.py script with the 1.2 line of > relax (subversion repository). > > The data was re

The use of a pdb with the sphere diffusion tensor

Hi, I am now helping someone to start with relax and got into a question about the full_analysis.py script. In the full_analysis.py script, the following code appears at line 550 : # Load the PDB file. if not local_tm: pdb(name, PDB_FILE) For a local tm, no PDB file is needed. That's logic

Re: The use of a pdb with the sphere diffusion tensor

in the local tm model MI results. If not, there is a good chance that you have artificial motions! Regards, Edward On Jan 10, 2008 8:20 PM, Sebastien Morin <[EMAIL PROTECTED]> wrote: Hi, I am now helping someone to start with relax and got into a question about the full_analysis.py s

Re: The use of a pdb with the sphere diffusion tensor

cript proceeds... Am I right ? Séb :) Edward d'Auvergne wrote: On Jan 10, 2008 9:59 PM, Sebastien Morin <[EMAIL PROTECTED]> wrote: Thanks Ed ! Another similar would maybe ease life of users without PDB or with small proteins... We could add the possibility of not havin

Re: The use of a pdb with the sphere diffusion tensor

ot include not. The statement needed is that if the UNRES file exists, use it to deselect the residues. It currently say that if the UNRES file does not exist, use it to deselect the residues. Sorry, I should have seen that one. Regards, Edward On Jan 10, 2008 10:17 PM, Sebastien Morin <[EM

Model elimination

/packages/relax/generic_fns/monte_carlo.py", line 220, in error_analysis Xav = Xsum / float(n) ZeroDivisionError: float division == It seems 'n' was zero for at least one residue... Is this something tha

Re: Model elimination

ed to fix this problem, but I am very interested in why this situation occured in the first place. The only reason I can think of right now is that all 500 Monte Carlo simulations failed! If so, that would be impressive! Cheers, Edward On Jan 28, 2008 7:01 PM, Sebastien Morin <[EMAIL P

R1 and R2 for MF analysis

field (R1 and R2 only). Will the 5 measured information be used or will only the complete dataset from the first field be used and the incompelte dataset rejected ? Thanks ! Séb -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne

Spheroid diffusion tensor

'Dratio' show up (since I specified I wanted to work with this parameter instead) ? Thanks ! Séb -- 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 __

full_analysis.py

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

Rex vs magnetic field

gets associated with the highest magnetic field ? With the lowest ? Thanks for clarifying this issue ! Cheers, Séb -- Sebastien Morin Etudiant au PhD en biochimie Laboratoire de resonance magnetique nucleaire Dr Stephane Gagne CREFSIP (Universite Laval, Quebec, CANADA) 1-418-656-2131 #4530

Re: R1 and R2 for MF analysis

Hi again, Thanks for that also ! Cheers, Séb Edward d'Auvergne wrote: On Feb 8, 2008 4:54 PM, Sebastien Morin <[EMAIL PROTECTED]> wrote: Hi, I have a theoretical question about Model-Free analysis concerning the minimum amount of data required... In ModelFree, it is

Re: Spheroid diffusion tensor

. If you need, there are user functions which will convert between the formats, printing out the different parameters. Regards, Edward On Feb 8, 2008 5:39 PM, Sebastien Morin <[EMAIL PROTECTED]> wrote: Hi, I am trying to select a prolate spheroid diffusion tensor. I want to specify

Re: Rex vs magnetic field

ive, but the current design allows an advanced user to choose which frequency the Rex is reported for. Regards, Edward On Feb 18, 2008 4:57 AM, Sebastien Morin <[EMAIL PROTECTED]> wrote: Hi, I have a question concerning Rex and its magnetic field dependence vs how it is t