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 <[email protected]>: > >> 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 >>> [email protected] >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> relax (http://nmr-relax.com) >>> >>> This is the relax-users mailing list >>> [email protected] >>> >>> 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-users >>> >>> >> _______________________________________________ >> relax (http://nmr-relax.com) >> >> This is the relax-users mailing list >> [email protected] >> >> 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-users >> >> >> > > _______________________________________________ relax (http://nmr-relax.com) This is the relax-users mailing list [email protected] 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-users
