Re: [PyMOL] setting the stick radius to different widths for substrate and protein residues

Look up the stick_radius command and use separate selections for the substrate and protein. Stuart On Friday 11 January 2008 21:32, Satinder K. Singh wrote: > Hello, > > I am trying to make a figure in which the stick radius of the substrate > (say, 0.3) is ~twice as large as that of the surrou

Re: [PyMOL] separating multiple conformers

> unbond selection1, selection2 On Wednesday 29 August 2007 18:16, th...@brandeis.edu wrote: > Hi, > > I am modeling both an ADP and an AMP molecules in the same binding > site for my enzyme; occupancy at 50%. I am trying to represent both > molecules as sticks however pymol connects the atoms th

Re: [PyMOL] problem in saving images or session

I've found the CentOS (free RHEL) distro to work quite well. No issues with pymol aside from a single random coordinate write error that I was never able to replicate and hasn't occurred since on either of the two CentOS 4.5 systems I'm running. As for Fedora, I switched off of it about a year

[PyMOL] failure to save coordinates adjusted with edit tool

ng on or how to correct? Pymol version 0.99rc6 running on Linux (CentOS 4.4) Stuart Endo-Streeter __ Stuart T. Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu

Re: [PyMOL] hydrogen_add problem

You should take a look at the program Reduce from the Richardson lab at Duke, it adds protons and is written in C++. It will take a pdb and without requiring modification or formating add protons to it. Versions exist for Linux, Windows, MacOS X, Irix, and Sun-SPARC, and the source code is av

[PyMOL] programs to make pymol movies in Linux

Hello fellow users, I would like to make movies from saved png's from pymol, as per usual, but entirely on my RHEL box. For various reasons I do not want to use Quicktime on Windows or Mac (and yes, I have seen how well they can work), so can anyone recommend programs I can use to encode movie

Re: [PyMOL] Slowwwww ray

http://ads.osdn.com/?ad_id=7628&alloc_id=16845&op=click > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users -- Stuart Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu

Re: [PyMOL] pymol problems with python after FC4 update

Tech:(650)-872-0834 > . Fax:(650)-872-0273 Cell:(650)-346-1154 > . mailto:war...@delsci.com > > > -Original Message- > > From: pymol-users-ad...@lists.sourceforge.net > > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > > Stuart Endo-Streeter >

[PyMOL] pymol problems with python after FC4 update

Endo-Streeter Stuart Endo-Streeter Structural Biology and Biophysics Dept. Biochemistry LSRC C266 Duke University 919-681-1668 stuart.endostree...@duke.edu