Here's a screenshot of the color scale. It appears to me that the red and blue colors are fainter than it should be. I tried using the ramp_new command as follows, but it is not working for me.
ramp_new ramp1, pymol-generated, [-10, 0, 10], [red, white, blue] I would greatly appreciate any help.
<<inline: スクリーンショット（2011-02-23 14.37.54）.png>>
On 2011/02/22, at 23:23, Michael Lerner wrote: > Hi all, > > On Tue, Feb 22, 2011 at 8:00 AM, Schubert, Carsten [PRDUS] > <cschu...@its.jnj.com> wrote: > 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. > > I think this is likely the case. Due to a lot of feedback, the plugin > defaults changed to showing the solvent accessible surface a while ago (see > the checkboxes in the Molecular Surface section of the Visualization panel). > > 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. > > Many (most?) users of the plugin do indeed use PDB2PQR. It's worth noting > that the current version of the plugin allows you to specify command line > arguments to PDB2PQR (e.g. --ff=AMBER, etc. if you're interested in trying > out different force fields). > > Cheers, > > -Michael > > > 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 > > > > -- > Michael Lerner, Ph.D. > IRTA Postdoctoral Fellow > Laboratory of Computational Biology NIH/NHLBI > 5635 Fishers Lane, Room T909, MSC 9314 > Rockville, MD 20852 (UPS/FedEx/Reality) > Bethesda MD 20892-9314 (USPS)
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