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
<tlin...@nmr-relax.com> 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-addr...@gna.org>:
>
>> 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)
>>
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