[PyMOL] Still time to participate in the Teach-Discover-Treat 2014 Competition!

Time to participate in the Teach-Discover-Treat (TDT) 2014 Competition is running out! There are four exciting challenges that focus on developing and disseminating computational workflows for drug discovery of neglected diseases with a premium on reproducibility. Three cash prizes - plus partial

Re: [PyMOL] Color by conservation

Hi Matzov, the script assumed an old (incomplete) PyMOL API. I corrected the script, please download it again. Cheers, Thomas On 09 Jan 2014, at 16:27, Matzov Donna wrote: > I'm trying to use the script that is available on pymolwiki for colouring > residues according to conservation. It

[PyMOL] Color by conservation

I'm trying to use the script that is available on pymolwiki for colouring residues according to conservation. It wasn't very clear to me so I tried to do the given example: reinitialize import color_by_conservation # get some kinases fetch 1opk 3dtc 3p86 2eva 3efw, async=0 # turn on the sequen

Re: [PyMOL] How to automate RMSD calculation for large no of structures

Thanks, Carsten. I thought it would turn out to be something related to the paths, but couldn't put my finger on it. (I was able to run the script fine without either of those fixes on Incentive PyMOL 1.5.0 32-bit on a Win XP VirtualBox VM guest on a Mac OS 10.8 host. Not sure why that might

Re: [PyMOL] How to automate RMSD calculation for large no of structures

Hi Om, asides from the usual list of suspects like access permissions try double backslashes or a raw string in your path-filenames. Python on Windows is a bit peculiar in that respect. Read up on raw strings in the Python docs. Try wt_file = "D:\\STUDY\\STRUCTURE_PPT\\RMSD\\Pymol\\Original\\

Re: [PyMOL] How to automate RMSD calculation for large no of structures

Hello I am using the following script file: ### begin script ### from pymol import cmd from glob import glob # Edit these two variables with the paths to your files wt_file = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\Original\1APS.pdb" mut_glob = "D:\STUDY\STRUCTURE_PPT\RMSD\Pymol\models\1APS\1APS_*.