Hi Wataru Kagawa, The intensity of the colors depends on the values of the data and the color ranges on the color ramp. In fact, in editing mode, CTRL-dragging can control the upper/lower values of the ramp, effecting the coloring. On top of that, you can assign colors to different numerical values.
All that should matter in your case is that the actual values remain the same. Are they? If not, have you investigated changes to the algorithms or implementations? Last, for more help on ramps, see http://www.pymolwiki.org/index.php/Ramp_New. Cheers, -- Jason On Mon, Feb 21, 2011 at 10:04 PM, Wataru Kagawa <wkag...@aoni.waseda.jp> wrote: > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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
