Thank you for the suggestion. I've looked at the gamma setting, but it was 1.0, so the washed out effect is not because of the gamma setting. I've noticed that raytracing removes the washed out effect of the scale bar, but not so much of the protein surface color.
Is there by any chance that the "Color by potential on sol. acc. surf." function in APBS changed (calculation method, for example) compared with that of the previous APBS versions? On 2011/02/23, at 21:55, Schubert, Carsten [PRDUS] wrote: > Wataru, just a thought: Have you looked into the gamma setting in pymol? > Setting gamma to 4.0 from 1.0 and raytracing reproduces the washed out > effect. > > >> -----Original Message----- >> From: Wataru Kagawa [mailto:wkag...@aoni.waseda.jp] >> Sent: Tuesday, February 22, 2011 7:19 PM >> To: Michael Lerner >> Cc: Schubert, Carsten [PRDUS]; pymol-users@lists.sourceforge.net >> Subject: [PyMOL] Color scale changed in APBS? >> >> Thank you very much for the suggestions. >> I have been mapping the potential on the solvent accessible surface >> and displaying the molecular surface, both in the past and present. I >> have been using PDB2PQR (force field = AMBER) as well. I am wondering >> whether it is just a difference in the red and blue colors in the >> scale bar as Jason mentioned. >> >> Wataru >> >> >> 2011年2月22日火曜日 Michael Lerner mgler...@gmail.com: >>> Hi all, >>> >>> On Tue, Feb 22, 2011 at 8:00 AM, Schubert, Carsten [PRDUS] 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- >> us...@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) >>> >> >> ----------------------------------------------------------------------- >> ------- >> Free Software Download: 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. 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 > ------------------------------------------------------------------------------ Free Software Download: 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. 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