Re: [PyMOL] APBS surface data export
Hi Matt, PyMOL does not currently allow you to export the data mapped to the surface. However, the dx format is very straightforward. It follows a subset of the OpenDX standard, as described on the APBS site ( http://www.poissonboltzmann.org/file-formats/mesh-and-data-formats/opendx-scalar-data ). I don't know much about surface file formats, but the PyMOL wiki mentions ( http://www.pymolwiki.org/index.php/Surface#Exporting_Surface.2FMesh_Coordinates_to_File) that you can save surface coordinates to a file. It might be possible for a developer (you?) to convince PyMOL to write out the electrostatic potential along with whatever else it's writing to the .wrl file. Hope that helps, -Michael On Mon, Jan 31, 2011 at 7:03 PM, Matteo Pendleton znfin...@gmail.comwrote: Greetings, I'm looking to use an electrostatic surface map for downstream calculations and was wondering whether it's currently possible (after using APBSv2 to calculate a surface potential map) to export a mesh of data points in a list format with each data point's associated potential? If not, does anyone have an outline of the file layout for the pymol-generated.dx file so I could write my own script to do it? Thank you kindly, Matt Pendleton Independent Researcher New York, NY -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d ___ 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) -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ 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] APBS surface data export
Greetings, I'm looking to use an electrostatic surface map for downstream calculations and was wondering whether it's currently possible (after using APBSv2 to calculate a surface potential map) to export a mesh of data points in a list format with each data point's associated potential? If not, does anyone have an outline of the file layout for the pymol-generated.dx file so I could write my own script to do it? Thank you kindly, Matt Pendleton Independent Researcher New York, NY -- Special Offer-- Download ArcSight Logger for FREE (a $49 USD value)! Finally, a world-class log management solution at an even better price-free! Download using promo code Free_Logger_4_Dev2Dev. Offer expires February 28th, so secure your free ArcSight Logger TODAY! http://p.sf.net/sfu/arcsight-sfd2d___ 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] APBS surface
YesI have already done as wrote My question iswhat if I up load ligand surface with receptor structure? Will it, as I think, shows me the potential of ligand on the receptor surface (giving me as sort of negative of ligand surface on receptor's)??? Thank for your answer, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Mike Summers summ...@hhmi.umbc.edu A: Gianluigi Caltabiano chimic...@yahoo.it Inviato: Martedì 27 marzo 2007, 20:14:37 Oggetto: Re: [PyMOL] APBS surface You need to create individual proteins and then create maps for the individual protein; e.g, create A,(structure and residues_of_A_only) Mike On Tue, Mar 27, 2007 at 01:35:56PM +, Gianluigi Caltabiano wrote: Hi everyone, I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces. Everything works fine. My question is: I have uploaded the structure of protein A and the surface of protein B. What it shows to me is a blank surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, projecting potential values of protein's surface B on the surface of protein A, like having a negative of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- * Michael F. Summers Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 Phone: (410)-455-2527 FAX: (410)-455-1174 Email: summ...@hhmi.umbc.edu Web: www.hhmi.umbc.edu ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html
Re: [PyMOL] APBS surface
PyMOL doesn't know where the electrostatic potential map comes from. If you load up a map and a structure, it will show the potential from that map on that structure. On 4/2/07, Gianluigi Caltabiano chimic...@yahoo.it wrote: YesI have already done as wrote My question iswhat if I up load ligand surface with receptor structure? Will it, as I think, shows me the potential of ligand on the receptor surface (giving me as sort of negative of ligand surface on receptor's)??? Thank for your answer, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Mike Summers summ...@hhmi.umbc.edu A: Gianluigi Caltabiano chimic...@yahoo.it Inviato: Martedì 27 marzo 2007, 20:14:37 Oggetto: Re: [PyMOL] APBS surface You need to create individual proteins and then create maps for the individual protein; e.g, create A,(structure and residues_of_A_only) Mike On Tue, Mar 27, 2007 at 01:35:56PM +, Gianluigi Caltabiano wrote: Hi everyone, I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces. Everything works fine. My question is: I have uploaded the structure of protein A and the surface of protein B. What it shows to me is a blank surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, projecting potential values of protein's surface B on the surface of protein A, like having a negative of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- * Michael F. Summers Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 Phone: (410)-455-2527 FAX: (410)-455-1174 Email: summ...@hhmi.umbc.edu Web: www.hhmi.umbc.edu L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net
Re: [PyMOL] APBS surface
OK...it's as I thought. That is uploading the wrong structure it shows me the map from the ligand but on receptors VdW surface. Thanks all, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Michael Lerner mgler...@gmail.com A: Gianluigi Caltabiano chimic...@yahoo.it Cc: pymol-users@lists.sourceforge.net Inviato: Lunedì 2 aprile 2007, 15:40:24 Oggetto: Re: [PyMOL] APBS surface PyMOL doesn't know where the electrostatic potential map comes from. If you load up a map and a structure, it will show the potential from that map on that structure. On 4/2/07, Gianluigi Caltabiano chimic...@yahoo.it wrote: YesI have already done as wrote My question iswhat if I up load ligand surface with receptor structure? Will it, as I think, shows me the potential of ligand on the receptor surface (giving me as sort of negative of ligand surface on receptor's)??? Thank for your answer, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain - Messaggio originale - Da: Mike Summers summ...@hhmi.umbc.edu A: Gianluigi Caltabiano chimic...@yahoo.it Inviato: Martedì 27 marzo 2007, 20:14:37 Oggetto: Re: [PyMOL] APBS surface You need to create individual proteins and then create maps for the individual protein; e.g, create A,(structure and residues_of_A_only) Mike On Tue, Mar 27, 2007 at 01:35:56PM +, Gianluigi Caltabiano wrote: Hi everyone, I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces. Everything works fine. My question is: I have uploaded the structure of protein A and the surface of protein B. What it shows to me is a blank surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, projecting potential values of protein's surface B on the surface of protein A, like having a negative of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- * Michael F. Summers Department of Chemistry and Biochemistry and Howard Hughes Medical Institute University of Maryland Baltimore County 1000 Hilltop Circle Baltimore, MD 21250 Phone: (410)-455-2527 FAX: (410)-455-1174 Email: summ...@hhmi.umbc.edu Web: www.hhmi.umbc.edu L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users -- Biophysics Graduate Student Carlson Lab, University of Michigan http://www.umich.edu/~mlerner http://lernerclan.net ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html
[PyMOL] APBS surface
Hi everyone, I am working with a protein-protein complex and I have calculated for each protein, let's say A and B, apbs electrostatic surfaces. Everything works fine. My question is: I have uploaded the structure of protein A and the surface of protein B. What it shows to me is a blank surface for most of the protein A but the part where protein B interact whit it. I think, but I would have confimations, that I am, in some way, projecting potential values of protein's surface B on the surface of protein A, like having a negative of the B interactions. It seems it works like this since I know both rotein's interacting residues and now I am facing interacting patch of residues from protein B on their counnter part on protein A. Am I wrong? Thank for your answer, in advance, Gianluigi Caltabiano Lab of Computational Medicine, BioStatistic Dept. UAB, Universitat Autonoma de Barcelona Spain ___ L'email della prossima generazione? Puoi averla con la nuova Yahoo! Mail: http://it.docs.yahoo.com/nowyoucan.html
[PyMOL] pymol apbs - surface numbers
Douglas Kojetin asked the following question on February 9, 2005: For example, the molecular surface numbers default to -1, 0 and 1. If they are changed to -5, 0 and 5, the displayed surface looks less charged than that displayed with the default numbers. What do the numbers mean? I'm not an expert on this, but the eletrostatic potential at the surface is often expressed in kT/e and that is also the unit listed in the header of the .dx file created by APBS. So my guess is that the numbers represent kT/e. When the surface potentials are displayed in PyMOL a linear interpolation is used to display the colors (completely red at or below -1 kT/e and completely blue at or above +1 kT/e). If you change the numbers from -1,0,+1 to -5,0,+1 an eletrostatic potential of -1 kT/e will no longer be completely red but instead somewhere inbetween red and white and that is why your protein will *look* less charged (the actuaæ potentials are of course identical, it is only their representation that is changed). Other factors that are likely to affect the electrostatic potential are the dielectric constants of the molecule (protein) and solvent, the temperature (298.15 K for a somewhat high room-temperature of 25'C, 310.15 K for human body temperature of 37'C) and the ionic strength. All these parameters can be set in the APBS tools plugin or directly in the APBS input (.in) file. Kind Regards, ./ Kristoffer
