Re: [PyMOL] installation trouble - SOLVED!!!
Hi Warren and all, I finally managed to solve my problem: here'e where I found the inspiration: http://discuss.pcmag.com/forums/1004327277/ShowPost.aspx The setup utility is a 16-bit app (as you have guessed), and it may gag if the path to its home folder is too long I simply moved the installation files to a short path (namely C:\) and renamed the directory containing the setup.exe of Pymol into Pymol (to make the path even shorter) and the installation was successfull!!! Hope this can help somebody else in the list... A. Angelo Favia wrote: 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
[PyMOL] surface coloring fails with gradient loaded
Hi there, i am trying to render fieldlines and sf potential together in a movie. The movie setup is like this: import os set gradient_spacing=5 load ProtOut.pdb,prot load trajshort.xtc,prot mset 1 -7 show surface set surface_solvent=1 for a in range(1,7): cmd.mdo(a,delete flines;delete dxmap;delete dxmap2;delete rmp;delete rmp2;save prot.pdb,prot;os.system(\pdb2pqr --ff=amber prot.pdb prot.pqrlog.txt\);os.system(\apbs apbs.inlog.txt\);load apbsout.dx,dxmap;load apbsout.dx,dxmap2;ramp_new rmp,dxmap, [-1.5,-0.75,0];ramp_new rmp2,dxmap,[-10,0,10];gradient flines,dxmap,-10,10,prot,carve=15;color rmp,flines;set surface_color=rmp,prot) set ray_trace_frames=1 set cache_frames=1 mclear Is there anything wrong on this setup? the surface is always white. If i do a show surface in every frame, then it seems to me as if the surface is calculated for all frames (600 in total). This is too slow to do it on every step. Any ideas? Cheers Martin
Re: [PyMOL] surface coloring fails with gradient loaded
Martin, Just FYI, the gradient display in PyMOL you and I have been working on is still too immature to be considered supportable or supported. Indeed, prior to your post, you were one of the few PyMOL users even aware of it. For everyone else, I suppose I should announce that one of the many new features pending for PyMOL 1.0 is the ability to display fieldlines in maps such as illustrated here: http://pymol.sf.net/pmimag/fieldlines.jpg The bugs are still being worked out, but usage parallels that of isomesh with ramp-based coloring by map potential. If you have SVN source, then gradient ? for usage. Note that this feature will not be supported by DeLano Scientific until after the 1.0 release. As for your question, mdo movie commands should be limited to localized state changes within PyMOL. Performing I/O or running external system calls (e.g. APBS) within a movie command is likely to not work, and may cause trouble, such crashes or hangs. The way to approach your need is to either precompute and preload all of your maps into PyMOL states (impractical for 600 maps), or to write a Python script which takes over from PyMOL in terms of sequencing, performing electrostatics, calculations, and rendering the movie. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Martin Höfling Sent: Friday, December 15, 2006 8:01 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface coloring fails with gradient loaded Hi there, i am trying to render fieldlines and sf potential together in a movie. The movie setup is like this: import os set gradient_spacing=5 load ProtOut.pdb,prot load trajshort.xtc,prot mset 1 -7 show surface set surface_solvent=1 for a in range(1,7): cmd.mdo(a,delete flines;delete dxmap;delete dxmap2;delete rmp;delete rmp2;save prot.pdb,prot;os.system(\pdb2pqr --ff=amber prot.pdb prot.pqrlog.txt\);os.system(\apbs apbs.inlog.txt\);load apbsout.dx,dxmap;load apbsout.dx,dxmap2;ramp_new rmp,dxmap, [-1.5,-0.75,0];ramp_new rmp2,dxmap,[-10,0,10];gradient flines,dxmap,-10,10,prot,carve=15;color rmp,flines;set surface_color=rmp,prot) set ray_trace_frames=1 set cache_frames=1 mclear Is there anything wrong on this setup? the surface is always white. If i do a show surface in every frame, then it seems to me as if the surface is calculated for all frames (600 in total). This is too slow to do it on every step. Any ideas? Cheers Martin - 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] Why does the sculpting feature not work?
Matt, Three points: (1) PyMOL's sculpting feature isn't a forcefield, so it is best to clean up any pose you sculpt with a molecular mechanics forcefield minimization afterwards (using external software, such as the Swiss PDB viewer). (2) Unless bonding information is provided in the file, PyMOL connects atoms based on distances. Depending upon your perspective, this is either an annoying limitation or a welcome warning that the structure you've loaded is nonphysical (or at least, far from equilibrium). (3) To save PDB files with explicit bonding and valences using the multi-CONECT convention, set pdb_conect_all before saving the file. Unfortunately, this feature may be broken or missing in noncurrent builds. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Matt Wagner Sent: Thursday, December 14, 2006 1:03 PM To: pymol-users@lists.sourceforge.net Subject: [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 - 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
[PyMOL] A suggestion on molecule selection
Hi, When two SDF files, each of which contains multiple entries, are loaded, it seems PyMOL can only display the same frames from the two objects. It goes like frame 1 in obj 1 and frame 1 in obj 2, and cannot do like frame 1 in obj 1 and frame 3 in obj 2. I was wondering if there is a way to get around. Thanks a lot, Frank
Re: [PyMOL] A suggestion on molecule selection
Frank, set state, state-number, object-name set state, obj1, 1 set state, obj2, 3 You can also use the freeze and thaw options in the object's action menu to freeze an object into the current state independent of the global state. Cheers, Warren From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of S. Frank Yan Sent: Friday, December 15, 2006 4:08 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] A suggestion on molecule selection Hi, When two SDF files, each of which contains multiple entries, are loaded, it seems PyMOL can only display the same frames from the two objects. It goes like frame 1 in obj 1 and frame 1 in obj 2, and cannot do like frame 1 in obj 1 and frame 3 in obj 2. I was wondering if there is a way to get around. Thanks a lot, Frank
