Hello all, Here is a simple script that automates the electrostatic potential surface generation using Gromacs, MEAD, and Pymol for visualization. It's exclusively based off of the post by Esben Peter Friis: http://sourceforge.net/mailarchive/forum.php?forum_id=60&max_rows=25&style=flat&viewmonth=200307&viewday=9
It requires you to massage your pdb file a bit, but it gets the job done. Please glance at the comments in the script to see what I mean. Script: http://expert.ics.purdue.edu/~geders/utilities/pymol_electrostatic_surface.sh Screenshot: http://expert.ics.purdue.edu/~geders/utilities/pymol_electrostatic_surface.png ~Todd On Tue, 2003-12-16 at 16:04, Warren L. DeLano wrote: > Ruslan, > > PyMOL can't yet calculate the electrostatic surface, but it > can > display the potential as output by Grasp, Delphi, MEAD, or Zap. > > Cheers, > Warren > > > -- > mailto:war...@delanoscientific.com > Warren L. DeLano, Ph.D. > Principal Scientist > DeLano Scientific LLC > Voice (650)-346-1154 > Fax (650)-593-4020 > > > -----Original Message----- > > From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- > > ad...@lists.sourceforge.net] On Behalf Of Sanishvili, Ruslan > > Sent: Tuesday, December 16, 2003 8:29 AM > > To: Warren L. DeLano; pymol-users@lists.sourceforge.net > > Subject: [PyMOL] electrostatic surface > > > > Hi all, > > Inexplicably, I haven't been following the PyMol news lately. Does > it > > now calculate and display the electrostatic fields/surfaces of > proteins > > (a la GRASP, or similar)? If it does, starting from which version? > > Thanks, > > Nukri > > > > > > Ruslan Sanishvili (Nukri), Ph.D. > > > > GM/CA-CAT, Bld. 436, D007 > > Biosciences Division, ANL > > 9700 S. Cass Ave. > > Argonne, IL 60439 > > > > Tel: (630)252-0665 > > Fax: (630)252-0667 > > rsanishv...@anl.gov > > > > > > > > > > ------------------------------------------------------- > > This SF.net email is sponsored by: IBM Linux Tutorials. > > Become an expert in LINUX or just sharpen your skills. Sign up for > IBM's > > Free Linux Tutorials. Learn everything from the bash shell to sys > admin. > > Click now! http://ads.osdn.com/?ad_id78&alloc_id371&op=ick > > _______________________________________________ > > PyMOL-users mailing list > > PyMOL-users@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > ------------------------------------------------------- > This SF.net email is sponsored by: IBM Linux Tutorials. > Become an expert in LINUX or just sharpen your skills. Sign up for > IBM's > Free Linux Tutorials. Learn everything from the bash shell to sys > admin. > Click now! http://ads.osdn.com/?ad_id78&alloc_id371&op=ick > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > >
