Re: [PyMOL] Color scale changed in APBS?
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
Re: [PyMOL] Color scale changed in APBS?
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) -- 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
[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-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) -- 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
Re: [PyMOL] Color scale changed in APBS?
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) -- 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
