Hi Michael,
You can find it in the 'scripts' directory of the 1.3 repository
('~relax/scripts/code_validator').
Regards,
Séb
Michael Bieri wrote:
> Hi Edward
>
> Where do I find the code_validator script?
>
> Cheers
> Michael
>
>
> Edward d'Auvergne schrieb:
>
>> Hi,
>>
>> I would start by getting the script in shape to be included into the
>> sample scripts directory. Afterwards I would look at incorporating
>> things into the core of relax. The script needs to have a relax
>> copyright statement with your name and the date in it, as in the
>> full_analysis.py script. It should also pass the
>> scripts/code_validator script (with reasonable exceptions). Then it
>> can be added to the repository. Oh, a full and clear description at
>> the top would also be useful.
>>
>> Regards,
>>
>> Edward
>>
>>
>>
>> 2009/10/21 Michael Bieri <michael.bi...@gmx.ch>:
>>
>>
>>> Hi Edward
>>>
>>> I think it could be useful to incorporate the scripts to relax,
>>> especially the pymol macro. I was looking for these functions in relax
>>> and wrote them by myself as I could not execute them in relax.
>>>
>>> If you could tell me how I have to modify the script to get into the
>>> core of relax, I will write them. I think the command you proposed would
>>> be ok, but we could also include a parameter, where you can indicate the
>>> maximum (e.g.) Rex value of one state of the protein, so the color
>>> coding would be relative to each other and not only per conformation (or
>>> even we could load results file of, let say, free and bound
>>> conformation). Just let me know and I will work on it.
>>>
>>>
>>> Cheers
>>> Michael
>>>
>>>
>>> Edward d'Auvergne schrieb:
>>>
>>>
>>>> Hi Michael,
>>>>
>>>> That script is quite useful, I need to get a few of these into the
>>>> sample scripts directory. Note that the results that Boaz has are not
>>>> those of a complete analysis and should not be presented (the
>>>> diffusion tensor is not optimised so the results will be full of
>>>> artifacts). One point with this script, I would recommend abstracting
>>>> the model. In model-free analysis, the model which has been selected
>>>> is not really important, rather the motions that are reported. For
>>>> example model m2 can nicely approximate model m5 and if noise makes
>>>> the slower motion statistically insignificant, that does not mean that
>>>> the motion is not there. I have added my script for Molmol macros to
>>>> the relax sample_scripts directory
>>>> (http://svn.gna.org/viewcvs/relax/1.3/sample_scripts/mf_molmol_plot.py?rev=9566&view=log)
>>>> which shows this.
>>>>
>>>> I was wondering if you would like to try to get your script into
>>>> relax? It could be quite useful to have, but there are a few things
>>>> that would need to be done. For example the Pymol macros would be
>>>> better implemented directly in relax rather than in the script. I.e.
>>>> there is the pymol.write() user function which currently does nothing.
>>>> This could be implemented so the user types something like:
>>>>
>>>> relax> pymol.write(data_type='amp_fast', style='bieri',
>>>> colour_start='red', colour_end='blue', force=True)
>>>> relax> pymol.write(data_type='time_slow', style='bieri',
>>>> colour_start='red', colour_end='blue', force=True)
>>>>
>>>> This could simply mimic the current molmol code but replacing the
>>>> contents with what you have in your script. I could add the script as
>>>> is, if it passes the code validator in 'scripts/code_validator', and
>>>> then this idea for incorporating your code into the core of relax
>>>> explored later. What do you think?
>>>>
>>>> Regards,
>>>>
>>>> Edward
>>>>
>>>>
>>>> 2009/9/17 Michael Bieri <michael.bi...@gmx.ch>:
>>>>
>>>>
>>>>
>>>>> Hi Boaz
>>>>>
>>>>> There are many data present in the result file obtained by relax (final
>>>>> run
>>>>> of full_analysis.py).
>>>>>
>>>>> To extract the data I am interested, I'm created the following script:
>>>>> final_data_extraction.py (see attachment).
>>>>>
>>>>> Just navigate to your final run directory, where the file results.bz2 is
>>>>> located, and copy your pdb file and this script into it. Then run the
>>>>> script
>>>>> using the command "relax final_data_extraction.py".
>>>>>
>>>>> This will create a table with Residue Numer - Model - S2 - Rex as well as
>>>>> single data files and grace plots. Furtermore, it calculates the diffucion
>>>>> tensor pdb and generates PyMol macros to visualize the S2 and Rex values
>>>>> in
>>>>> PyMol (just run the macros in PyMol terminal by the command "@s2.pml").
>>>>>
>>>>> The script works with relax 1.3.4 (not tested with 1.3.3).
>>>>>
>>>>> I hope this script may help you! There is more that can be incorporated.
>>>>>
>>>>> Cheers
>>>>> Michael
>>>>>
>>>>>
>>>>> Michael Bieri, PhD
>>>>> Department of Biochemistry and Molecular Biology
>>>>> Bio21 Molecular Science and Biotechnology Institute
>>>>> The University of Melbourne, 30 Flemington Road
>>>>> Parkville, Victoria 3010, Australia
>>>>>
>>>>> Tel.: +61 3 8334 2256
>>>>>
>>>>> http://www.biochemistry.unimelb.edu.au
>>>>>
>>>>>
>>>>>
>>>>> Boaz Shapira wrote:
>>>>>
>>>>>
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I just installed relax and tried to figure out how it works (couldn't).
>>>>>> I have no idea about python and I don't mind to keep it that way unless i
>>>>>> have no other choice.
>>>>>> Still, I tried to play with the examples and couldn't make it work (the
>>>>>> relax --text-suite didn't give me error)
>>>>>>
>>>>>>
>>>>>> I tried to run model-free.py from the relax prompt but it gives me error.
>>>>>> " Traceback (most recent call last):
>>>>>> File "<console>", line 1, in <module>
>>>>>> NameError: name 'model' is not defined "
>>>>>>
>>>>>> Then I copied line by line and it did work.
>>>>>> It save it in a .bz2 format.
>>>>>> Now If I want to read the data what format should I use?
>>>>>> It looks like a source html file.
>>>>>>
>>>>>>
>>>>>> In general I collected data on two fields and want to analyze the data
>>>>>> with a black box (the full_analysis.py ?)
>>>>>> I have the input files in the right format as in the examples
>>>>>> I have the pdb file
>>>>>>
>>>>>> Is it possible to simply run a black-box that will give me an output:
>>>>>> List of the residues with the best model for each, the values for this
>>>>>> model (S2, tau ...), the goodness of the fitting, and
>>>>>> the overall diffusion tensor?
>>>>>> This black box will also reject "bad" relaxation data.
>>>>>> and all of that will be given in a text file?
>>>>>>
>>>>>> It is too much to ask?
>>>>>>
>>>>>> Thank you,
>>>>>>
>>>>>> Boaz
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------
>>>>>> Boaz Shapira PhD
>>>>>> Complex Carbohydrate Research Center
>>>>>> University of Georgia
>>>>>> 315 Riverbend Rd
>>>>>> Athens, GA 30602-4712
>>>>>> 706-542-6286
>>>>>> bshap...@ccrc.uga.edu
>>>>>> ------------------------------------------------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> relax (http://nmr-relax.com)
>>>>>>
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>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> relax (http://nmr-relax.com)
>>>>>
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>>>>>
>>>>>
>>>>>
>>>>
>>>>
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>
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--
Sébastien Morin
PhD Student
S. Gagné NMR Laboratory
Université Laval & PROTEO
Québec, Canada
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