stien
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|| Sebastien Morin ||
||| Etudiant au doctorat en biochimie |||
Laboratoire de resonance magnetique nucleaire
| Dr Stephane Gagne |
CREFSIP (Universite
on options,
visit the list information page at
https://mail.gna.org/listinfo/relax-users
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|| Sebastien Morin ||
||| Etudiant au doctorat en biochimie |||
Laboratoire de resonance magnetique nucleaire
|
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
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|| Sebastien Morin ||
||| Etudiant au doctorat en biochimie |||
Laboratoire de resonance magnetique nucleaire
| Dr Stephane Gagne |
CREFSIP (Universite Laval
. 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
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
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
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
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
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
for helping me solve this obviously easy issue...
Sébastien :)
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|| Sebastien Morin ||
||| Etu
:)
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
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
timescale motions) from my data using reduced
spectral density mapping at those three fields ?
Thanks !!
Sébastien :)
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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
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
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
>&
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
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
?
Thanks !
Sébastien
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|| Sebastien Morin ||
||| Etudiant au PhD en biochimie |||
Laboratoire de resonance magnetique nucleaire
| Dr Stephane Gagne |
t;>>>>>> full_analysis.py script in the relax repository (to both
>>>>>>>>>>
>>>>> the 1.2
>>>>>
>>>>>>>>> and
>>>>>>>>>
model-free analysis using ModelFree).
Thanks !
Sébastien :)
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|| Sebastien Morin ||
||| Etudiant au
so, in the case of duplicates or triplicates, should one use the same
approcah ?
Thanks !
Séb :)
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|| Sebas
would, on the contrary, speed
up calculations...
Thanks for ideas !
Sébastien :)
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|| Sebast
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
---------
>>
>> 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"
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
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
>&
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
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
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,
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
(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
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
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).
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
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
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
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
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
/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
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
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
'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
__
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
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
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
. 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
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
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