Re: [PyMOL] translating cgo text
Hi, A workaround may be to wrap the cgo object in a python object, with a reload function, as well as with transformation functions. class CGOWrap: cgoObject = [] name= [] def translate(self,vector): def rotate(self,matrix): def reload(self) ...etc... The most difficult thing is to extract from a pure cgo object where the coordinates are... Tsjerk On 4/1/07, DeLano Scientific del...@delsci.info wrote: Jennifer, Having glanced at the code, this is clearly not yet possible -- only molecule objects, atoms, and labels can currently be dragged about. However, eventually it will be possible to drag and animate all object types. Cheers, Warren -- DeLano Scientific LLC Subscriber Support Services mailto:del...@delsci.info Not yet a PyMOL Subscriber, but want to support the project? Email sa...@delsci.com to quote your lab, school, or employer. Thank you for sponsoring this open-source endeavor! -WLD From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of jennifer.pfings...@uchsc.edu Sent: Friday, March 30, 2007 1:41 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] translating cgo text Hi Everyone, I hope that this issue is a relatively simple on to resolve. Is it possible to move cgo text in pymol when a pdb is displayed? How do I do perform this task? Any help you can provide is always greatly appreciated! Thank you in advanced, jennifer pfingsten - 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623
[PyMOL] Different states with different representation?
Hello every-body, Just a quick question: Is it possible to display the different states of a molecule with different types of representation (for exemple: sticks and spheres)? Thank you all. Fred
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
