Hi Edward,
thank you so much for coming up with a solution so quickly! Your script
is perfect and so fast!
(I am sorry for the late reply but I was out of office the last days.)
Best regards,
Christina
Am 11/23/2015 um 10:27 AM schrieb Edward d'Auvergne:
Hi Christina,
I've had a look at your support request
(https://gna.org/support/?3303) and have tried to come up with a
solution:
http://article.gmane.org/gmane.science.nmr.relax.scm/25842
For this, I had to reintroduce the "<mol name="GAB">" and "</mol>"
tags in the XML results file, otherwise relax cannot read the file
correctly. The newly introduced sample script is quite simple:
http://svn.gna.org/viewcvs/relax/trunk/sample_scripts/model_free/back_calculate.py?view=markup&pathrev=28091
It is simply:
"""
# Load the results as a state file.
state.load('results')
# Loop over each relaxation data set.
for ri_id in cdp.ri_ids:
# Back calculate the relaxation data.
relax_data.back_calc(ri_id=ri_id, ri_type=cdp.ri_type[ri_id],
frq=cdp.spectrometer_frq[ri_id])
# Write the data.
relax_data.write(ri_id=ri_id, file='%s.out' % ri_id.lower(),
bc=True, force=True)
"""
This loads the results file and then uses the information in the
current data pipe to loop over and back-calculate each relaxation data
point. Note the important bc=True flag used in the relax_data.write
user function (http://www.nmr-relax.com/manual/relax_data_write.html).
Is this script sufficient?
Regards,
Edward
On 20 November 2015 at 14:26, Troels Emtekær Linnet
<tlinnet@xxxxxxxxxxxxx> wrote:
Dear Christina.
Thank you for your contribution.
I am sure this will be of benefits to other users, and a good reference for
automatic back-calculation of spin relaxation data.
Time is always precious and so the development of this can take some time.
But it is essential that the support request is described and including a
potential fix.
This will make the solution easier.
Thank you again. :)
May the "good results" be with you and happy "relaxing".
Best
Troels
2015-11-20 11:36 GMT+01:00 Christina Möller <
NO-REPLY.INVALID-ADDRESS@xxxxxxx>:
URL:
<http://gna.org/support/?3303>
Summary: Automatic back-calculation of spin relaxation
data
Project: relax
Submitted by: cmoeller
Submitted on: Fri 20 Nov 2015 10:36:06 AM UTC
Category: Feature request
Priority: 5 - Normal
Severity: 1 - Wish
Status: None
Assigned to: None
Originator Email:
Open/Closed: Open
Discussion Lock: Any
Operating System: GNU/Linux
_______________________________________________________
Details:
After the full model-free analysis of relaxation data using the
dauvergne_protocol.py script it would be interesting to compare the
back-calculated values to the original experimental values.
The generate_ri.py script back-calculates the relaxation data from given
residue-specific s2, s2f, s2s, te, tf, ts values that are obtained from
the
model-free analysis. The generate_ri.py script that can be found in the
sample
scripts/model-free folder generates back-calculated data for just one
residue-specific set of parameters. To obtain the back-calculated data for
i.e. 80 residues the script has to be used 80 times. It would be more
efficient if the script is started only once and the residue-specific
parameters are loaded automatically for each residue in order to generate
the
back-calculated values for all residues.
Attached you can find some example data.
A colleague who is more familiar with python than me tried to find a
solution
and edited the generate_ri.py script. Attached you can find the modified
script named generate_ri_mod.py. To run this script the results.py script
is
needed because it extracts the data from the results.bz2 file. This
modified
script back-calculates the values automatically and generates an output
file
named relaxation_data.dat containing back-calculated values for all
residues.
You will probably have a solution which is more consistent with your
programming of relax.
_______________________________________________________
File Attachments:
-------------------------------------------------------
Date: Fri 20 Nov 2015 10:36:06 AM UTC Name: results.bz2 Size: 344kB
By:
cmoeller
Example data and used relax script
<http://gna.org/support/download.php?file_id=25821>
-------------------------------------------------------
Date: Fri 20 Nov 2015 10:36:06 AM UTC Name: generate_ri.py Size: 5kB
By:
cmoeller
Example data and used relax script
<http://gna.org/support/download.php?file_id=25822>
-------------------------------------------------------
Date: Fri 20 Nov 2015 10:36:06 AM UTC Name: generate_ri_mod.py Size: 7kB
By: cmoeller
Example data and used relax script
<http://gna.org/support/download.php?file_id=25823>
-------------------------------------------------------
Date: Fri 20 Nov 2015 10:36:06 AM UTC Name: results.py Size: 4kB By:
cmoeller
Example data and used relax script
<http://gna.org/support/download.php?file_id=25824>
_______________________________________________________
Reply to this item at:
<http://gna.org/support/?3303>
_______________________________________________
Message sent via/by Gna!
http://gna.org/
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-devel mailing list
relax-devel@xxxxxxx
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-devel
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-devel mailing list
relax-devel@xxxxxxx
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-devel
--
------------------------------------------------------------
Christina Möller
ICS-6 / Structural Biochemistry
Forschungszentrum Jülich
D-52425 Jülich
GERMANY
E-mail: c.moeller@xxxxxxxxxxxxx
Tel.: +49-2461-619387
Fax +49-2461-619387
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
WG: [sr #3303] Automatic back-calculation of spin relaxation data