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 <[email protected]>: > 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 > _______________________________________________ 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
