[PyMOL] Copy a selection for a new molecule?
Hi All in one of my scripts I have a problem with getting a selection for a new molecule which is created from a copy of another which also have a selection. In the first one a selection is made of the user, but after creating a new molecule from the whole of the old, I cannot use the old selection directly. I could of course specify the selection in the script itself, but for interactive use of user-defined selections I've tried stored.list=[] cmd.iterate(selection+ name ca,stored.list.append(resi)) print stored.list cmd.select(newsel,none) for resi in stored.list: print resi cmd.select(newsel, newsel or (molecule2 resi %s)%resi) Is there a more elegant and or robust way of doing this? I'm especially tired of the iterating through the list for each new molecule. Best Regards Esben Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited
Re: [PyMOL] installation trouble
Dear all, We installed yesterday six brand new Dell PCs with winXPpro/SP2 (fully updated) and encounter exactly the same error (and also...the solutions in the pymol wiki didn't help us so far). Anyone a solution? Thanks in advance. Best, Joris Beld Hilvert Group, ETH Zürich Angelo D Favia wrote: I already tried all of the solution at the website but they didn't work for me. The error message still appears. A. DeLano Scientific wrote: http://www.pymolwiki.org/index.php/Windows_Install -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Angelo D Favia Sent: Monday, December 11, 2006 9:39 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] installation trouble Hi all, I'm trying to install the latest version of pymol on my laptop (Windows XP pro SP2) but there seem to be something wrong. I get the following error message in a window whose title is Can't run 16-bit Windows program: Cannot find file C:\***\pymol-0_99rc6-bin-win32\SETUP.EXE (or one of its components). Check to ensure the path and filename are correct and that all required libraries are available. Any clue about this error?? thanks angelo -- Angelo D Favia, PhD www.ebi.ac.uk/~afavia - 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 - 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
Re: [PyMOL] installation trouble
Joris, Some Dell systems are uniquely afflicted -- according to another Dell XP/SP2 owner: I found the solution, apparently the installer gets screwed up by some software that Dell installs as part of their standard build. The fix can be found at: http://www.wave.com/support/CSC/CustomerService/Documents/DM-010.htm I followed the steps in the above url and PyMol installed without a hitch. A detailed discussion on the topic can be found at: http://forum.installsite.net/index.php?s=03b224df496bbf806744f85d27c687e9sh owtopic=14905st=0#entry41109 Joris, do please follow up to the list if this solves your problem... Cheers, Delsci _ From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Joris Beld Sent: Thursday, December 14, 2006 7:11 AM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] installation trouble Dear all, We installed yesterday six brand new Dell PCs with winXPpro/SP2 (fully updated) and encounter exactly the same error (and also...the solutions in the pymol wiki didn't help us so far). Anyone a solution? Thanks in advance. Best, Joris Beld Hilvert Group, ETH Zürich Angelo D Favia wrote: I already tried all of the solution at the website but they didn't work for me. The error message still appears. A. DeLano Scientific wrote: http://www.pymolwiki.org/index.php/Windows_Install http://www.pymolwiki.org/index.php/Windows_Install -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Angelo D Favia Sent: Monday, December 11, 2006 9:39 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] installation trouble Hi all, I'm trying to install the latest version of pymol on my laptop (Windows XP pro SP2) but there seem to be something wrong. I get the following error message in a window whose title is Can't run 16-bit Windows program: Cannot find file C:\***\pymol-0_99rc6-bin-win32\SETUP.EXE (or one of its components). Check to ensure the path and filename are correct and that all required libraries are available. Any clue about this error?? thanks angelo -- Angelo D Favia, PhD www.ebi.ac.uk/~afavia - 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.php http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV p=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users - 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.php http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV p=sourceforgeCID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Copy a selection for a new molecule?
Esben, load molA.pdb select selA, resi 100-200 create molAcpy, molA select selAcpy, selA in molAcpy Note that this will only work if the atom identifiers: name, resi, resn, segi, chain are all unique. The in operator does not distinguish based on the alt (alternate conformer) property, so all matching conformers for a residue will be selected in the new selection if any were selected in the original. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Esben Jannik Bjerrum Sent: Thursday, December 14, 2006 6:54 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Copy a selection for a new molecule? Hi All in one of my scripts I have a problem with getting a selection for a new molecule which is created from a copy of another which also have a selection. In the first one a selection is made of the user, but after creating a new molecule from the whole of the old, I cannot use the old selection directly. I could of course specify the selection in the script itself, but for interactive use of user-defined selections I've tried stored.list=[] cmd.iterate(selection+ name ca,stored.list.append(resi)) print stored.list cmd.select(newsel,none) for resi in stored.list: print resi cmd.select(newsel, newsel or (molecule2 resi %s)%resi) Is there a more elegant and or robust way of doing this? I'm especially tired of the iterating through the list for each new molecule. Best Regards Esben Yahoo! Music Unlimited Access over 1 million songs. http://music.yahoo.com/unlimited - 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
Re: [PyMOL] installation trouble
I've got a Dell D820. I tried but it didn't fix my problem... I went for the soft solution first (partial removal of the guilty software) and for the hard one (total removal) then. The same error appears...as nothing changed. A. DeLano Scientific wrote: Joris, Some Dell systems are uniquely afflicted -- according to another Dell XP/SP2 owner: I found the solution, apparently the installer gets screwed up by some software that Dell installs as part of their standard build. The fix can be found at: http://www.wave.com/support/CSC/CustomerService/Documents/DM-010.htm I followed the steps in the above url and PyMol installed without a hitch. A detailed discussion on the topic can be found at: http://forum.installsite.net/index.php?s=03b224df496bbf806744f85d27c687e9showtopic=14905st=0#entry41109; Joris, do please follow up to the list if this solves your problem... Cheers, Delsci *From:* pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] *On Behalf Of *Joris Beld *Sent:* Thursday, December 14, 2006 7:11 AM *To:* pymol-users@lists.sourceforge.net *Subject:* Re: [PyMOL] installation trouble Dear all, We installed yesterday six brand new Dell PCs with winXPpro/SP2 (fully updated) and encounter exactly the same error (and also...the solutions in the pymol wiki didn't help us so far). Anyone a solution? Thanks in advance. Best, Joris Beld Hilvert Group, ETH Zürich Angelo D Favia wrote: I already tried all of the solution at the website but they didn't work for me. The error message still appears. A. DeLano Scientific wrote: http://www.pymolwiki.org/index.php/Windows_Install -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Angelo D Favia Sent: Monday, December 11, 2006 9:39 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] installation trouble Hi all, I'm trying to install the latest version of pymol on my laptop (Windows XP pro SP2) but there seem to be something wrong. I get the following error message in a window whose title is Can't run 16-bit Windows program: Cannot find file C:\***\pymol-0_99rc6-bin-win32\SETUP.EXE (or one of its components). Check to ensure the path and filename are correct and that all required libraries are available. Any clue about this error?? thanks angelo -- Angelo D Favia, PhD www.ebi.ac.uk/~afavia - 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 - 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 - 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 -- Angelo Favia, PhD www.ebi.ac.uk/~afavia
Re: [PyMOL] Coloring structure by hydrophobicity
Hi Andrew, regarding hydrophobicity coloring, we use the rTools from Kristian Rother. http://www.rubor.de/bioinf/pymol_extensions.html The coloring schemes are according to http://www.expasy.org/cgi-bin/protscale.pl It comes with a nice user interface, or on command prompt you would simply do something like color_protscale 10, selection where 10 is the coloring scheme (might differ in your installation): Normalized consensus hydrophobicity scale. Eisenberg D., Schwarz E., Komarony M., Wall R. J. Mol. Biol. 179:125-142(1984). (See also attached image) Cheers, Andreas Andrew D. Fant wrote: Afternoon all, I apologize if this has been hashed over on the list in the past. I haven't been keeping up like I used to. Is there a good way to calculate and color residues by hydrophobicity in pymol? A google search showed only a very simple script that was based entirely on a single-residue lookup table. I'm looking at a set of structure predictions, and it would be nice to easily see that a fold exposes a large patch of hydrophobic surface to solvent. Thanks, Andy -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 EMail: a...@biotec.tu-dresden.de inline: hydrophobicity.jpg
[PyMOL] Why does the sculpting feature not work?
Hi, I constructed a model (.pdb format) and attempted to eliminated some of the excessive contortions in the loop when opened in PYMOL. I was using Auto-sculpting to eliminate these contortions. All looked great, but when I saved my work to a .pdb file and opened it back up, it contained broken, stretched, and ugly bonds!!.Perhaps I have am not using the right tool for this task? When I open my model in Swiss PDB Viewer, all is fine. However, I need the graphics and great picture quality that PYMOL creates. Can you tell me a better approach to eliminating contortions in loops in PYMOL or perhaps another program that I should use with just as great graphics? Matt Wagner The Gogonea Group Cleveland, OH 44106 216-875-9723
