Hi Wataru, in addition to what Jason mentioned: Have you tried to look at the potential mapped on the solvent accessible surface and display the molecular surface? If you display the potential like this the colors will be much more muted, on the other hand this is the setting you will find most often displayed in the literature. Another option is to have a look at the charge distribution of your molecule in the actual PQR file. The potential distribution is dependent on the charging algorithm used. I would recommend using/looking into PDQ2PQR, which is available from the APBS website and compare this to the homegrown charging algorithm from PyMol or GRASP for that matter.
Hope I did not muddle the water too much Carsten > -----Original Message----- > From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp] > Sent: Monday, February 21, 2011 10:04 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Color scale changed in APBS? > > Dear PyMOL users: > > I recently used the APBS plugin (v1.3) to display the surface potential > of a protein. I noticed that the charged surfaces were much more > lightly colored, compared with the surface colors I have calculated in > the past (maybe a year ago?) on the same protein, using the same > softwares. The default settings and the same range (-10 kT to 10 kT) > were used in both cases. Has anyone experienced this? > > I would appreciate any help. > > Wataru > > > ----------------------------------------------------------------------- > ------- > Index, Search & Analyze Logs and other IT data in Real-Time with Splunk > Collect, index and harness all the fast moving IT data generated by > your > applications, servers and devices whether physical, virtual or in the > cloud. > Deliver compliance at lower cost and gain new business insights. > Free Software Download: http://p.sf.net/sfu/splunk-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------------------------ Index, Search & Analyze Logs and other IT data in Real-Time with Splunk Collect, index and harness all the fast moving IT data generated by your applications, servers and devices whether physical, virtual or in the cloud. Deliver compliance at lower cost and gain new business insights. Free Software Download: http://p.sf.net/sfu/splunk-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
