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 <[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
