Hi Christina,
I have now fixed the equation in the manual:
http://svn.gna.org/viewcvs/relax?view=revision&revision=28071
Thank you for reporting the error. For the
http://wiki.nmr-relax.com/CGS_versus_SI article, hopefully I'll one
day extend this to cover the differences in the equations in the NMR
literature. As Troels asked, could you give a few more details of
what you'd like to do? Where does the results.bz2 file come from?
Step-by-step points would be ideal. If it is from a model-free
analysis, open it in a text editor and see if the back calculated data
is not already there (in most cases it will be). Are you modifying
some values and then would like new back calculated data? These are
all important questions for determining how to create a new script
suited for your needs, for example to read in the results.bz2 file,
make the modifications you wish, back-calculate the data, and then
output it into text files.
Regards,
Edward
On 16 November 2015 at 10:33, Christina Möller <c.moel...@fz-juelich.de> wrote:
> Hi Troels,
>
> thanks for your support. I am using the generate_ri.py script to back
> calculate the relaxation data from given s2, s2f, s2s, te, tf, ts values to
> compare it to the original experimental data. I would like to know if it is
> easily possible to read in the parameters for each spin automatically from
> the results.bz2 file (obtained by the full model-free optimisation) or from
> lists, in order to run this script only once.
> So far, I executed the generate_ri.py script seperately for each residue and
> I obtained the back calculated data but this is certainly not the most
> efficient way.
>
> Best,
> Christina
>
>
>
>
>
> Am 11/15/2015 um 06:47 PM schrieb Troels Emtekær Linnet:
>>
>>
>> Dear Christina.
>>
>> I think Edward is on vacation, but maybe I can help.
>>
>> I have only worked on the dispersion part of relax and by no means expert
>> on the model free part.
>>
>> But I understand the data structure of relax and can maybe help with a
>> script for your analysis.
>>
>> Can you provide a description of where you are in the process, and what
>> you aim for.?
>>
>> Best Troels
>>
>> Den 13. nov. 2015 12.12 PM skrev "Christina Möller"
>> <c.moel...@fz-juelich.de <mailto:c.moel...@fz-juelich.de>>:
>>
>> Dear Edward,
>>
>> thank you so much for your recommendations and the really helpful wiki
>> article about the CGS and SI unit system. Now I understand the
>> equation
>> differences and successfully back-calculated my relaxation data.
>>
>> Furthermore, I used the generate_ri.py script and the back-calculated
>> values are close to the experimental data (as expected). I have to
>> admit
>> that I copied the motion parameters (s2,sf2,s2s,tf, etc) and the
>> associated model manually into the script and executed the script
>> several times for different residues. I am pretty sure that it is
>> possible to include one or several lists in order to automatically
>> update these parameters for each residue and run this script only one
>> time. Unfortunately, I was not able not find out how this works. Could
>> you give me an idea?
>>
>> Thanks,
>> Christina
>>
>>
>>
>> Am 11/05/2015 um 03:53 PM schrieb Edward d'Auvergne:
>>
>> Hi Christina,
>>
>> Please see below:
>>
>> On 5 November 2015 at 14:05, Christina Möller
>> <c.moel...@fz-juelich.de <mailto:c.moel...@fz-juelich.de>> wrote:
>>
>> Dear Edward and relax-users,
>>
>> I am sorry to ask you again for some advice to back
>> calculate the relaxation
>> data from the model parameter values. Here is what I tried
>> so far:
>> For the back calculation I loaded the final results
>> determined by the
>> automated analysis using the dauvergne_protocol.py into
>> the relax gui. Then
>> I selected the back_calc tool from user functions ->
>> relax_data.
>> After starting the back calculation without any entry
>> relax> relax_data.back_calc(ri_id=None, ri_type=None,
>> frq=None)
>> I get the following error message:
>> RelaxWarning: comparison to `None` will result in an
>> elementwise object
>> comparison in the future.
>>
>> This is a warning produced by more recent versions of the
>> numpy Python
>> package. It is harmless message about changes which will occur in
>> numpy, and it is safe to ignore. Note that I have fixed this
>> in the
>> source code repository and the fix will appear in the future
>> when I
>> release relax 4.0.1 (it is not present in relax 4.0.0 at
>> http://wiki.nmr-relax.com/Relax_4.0.0 ). This was first
>> reported at:
>>
>> [relax-users] RelaxWarning: comparison to `None` will
>> result in an
>> elementwise object comparison in the future (
>> http://thread.gmane.org/gmane.science.nmr.relax.user/1839 ).
>>
>> And the solution at:
>>
>> [relax-users] Re: RelaxWarning: comparison to `None` will
>> result
>> in an elementwise object comparison in the future (
>> http://thread.gmane.org/gmane.science.nmr.relax.user/1844 ).
>>
>>
>> If I put the frequency in
>> relax> relax_data.back_calc(ri_id=None, ri_type=None,
>> frq=599468076.0)
>> I get another error message
>> Traceback (most recent call last):
>> File
>>
>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/gui/interpreter.py",
>> line 306, in run
>> fn(*args, **kwds)
>> File
>>
>> "/opt/scisoft64/usr/lib/python2.7/site-packages/relax/pipe_control/relax_data.py",
>> line 132, in back_calc
>> spin.ri_data_bc[ri_id] =
>> api.back_calc_ri(spin_index=spin_index,
>> ri_id=ri_id, ri_type=ri_types[ri_id], frq=frqs[ri_id])
>> KeyError: 'R1_600'
>>
>> Can you give me a hint what I am doing wrong?
>>
>> I would suggest using the sample_scripts/model_free/generate_ri.py
>> sample script. The relax_data.back_calc user function
>> requires that
>> the relaxation data ID, the relaxation type, and frequency
>> arguments
>> be supplied to correctly calculate the desired data (see
>> http://www.nmr-relax.com/manual/relax_data_back_calc.html ).
>> Without
>> this information, relax cannot determine what you would like
>> to do.
>> Using the sample script would be the easiest option.
>>
>>
>> I know that the relaxation data can also be back
>> calculated using the
>> equations 7.3a - 7.8 in the relax manual (PDF), although
>> it is not that
>> trivial for an ellipsoid model because I need to determine
>> the weights. Is
>> there a reason why you define c=1/3(ωH*∆σ)^2 (eq. 7.5)
>> instead of
>> c=2/15(ωN*∆σ)^2 like it can be found in literature?
>>
>> These two factors come from using CGS vs. SI units. I have
>> mentioned
>> this issue before (see
>>
>> http://thread.gmane.org/gmane.science.nmr.relax.devel/1023/focus=1034
>> ). I have also started a stub wiki article to help explain these
>> differences - http://wiki.nmr-relax.com/CGS_versus_SI . In SI
>> units
>> the correct unit (squared) is (ω·∆σ)^2 / 3, and SI units are used
>> throughout relax. This has made some parts of relax more
>> difficult to
>> implement as there are many equations in the literature in CGS
>> units,
>> and the authors will often not identify this older system. Some
>> stubborn people just prefer the magnetic constant to be 1
>> rather than
>> µ0/(4π), and will not shift from the CGS metric system to the SI
>> metric system.
>>
>> Regards,
>>
>> Edward
>>
>>
>>
>> --
>> ------------------------------------------------------------
>> Christina Möller
>> ICS-6 / Structural Biochemistry
>> Forschungszentrum Jülich
>> D-52425 Jülich
>> GERMANY
>>
>> E-mail: c.moel...@fz-juelich.de <mailto:c.moel...@fz-juelich.de>
>> Tel.: +49-2461-619387 <tel:%2B49-2461-619387>
>> Fax +49-2461-619387 <tel:%2B49-2461-619387>
>>
>>
>>
>>
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>
>
> --
> ------------------------------------------------------------
> Christina Möller
> ICS-6 / Structural Biochemistry
> Forschungszentrum Jülich
> D-52425 Jülich
> GERMANY
>
> E-mail: c.moel...@fz-juelich.de
> Tel.: +49-2461-619387
> Fax +49-2461-619387
>
> _______________________________________________
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