Mark, Coloring by partial charge should work fine, provided that you supply partial charges to PyMOL...which isn't trivial. You could either assign them using the 'alter' command after loading a PDB or SDF file, or you could convert your molecule into a Chemical Python "model" object, assign them via Python, and then load the model back into PyMOL.
Coloring by electrostatic potential is something I am hoping to get into version 1.0...but PyMOL's current support for it is weak to non-existent. Cheers, Warren > -----Original Message----- > From: Mark Wall [mailto:mw...@diversa.com] > Sent: Thursday, October 24, 2002 12:25 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] color by partial charge? (electrostatics) > > > Hello, > > > Background > I want to create a surface colored by electrostatic > potential in PyMOL. > I can simulate this by coloring atoms by a formal charge which is > either 1, 0 or -1, ... > > color white > color blue, (fc; > 0.5) > color red, (fc; < -0.5) > show surface > > Of course this does not look like a surface colored by > Poisson-Boltzmann > calculated potentials > > Questions > 1. Can I color atoms by partial_charge? (this did not seem > to work for > me) > 2. Is there a better way using only PyMOL to approximate > P-B calculated > potentials? > > > Thanks, > Mark > > > > ------------------------------------------------------- > This sf.net email is sponsored by: Influence the future > of Java(TM) technology. Join the Java Community > Process(SM) (JCP(SM)) program now. > http://ads.sourceforge.net/cgi-bin/redirect.pl?sunm0003en > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
