Re: [PyMOL] pymol slow on linux PC
Dear all, Thanks for all the suggestions. - checked glxinfo and the startup log of pymol and it shows the loading of the propriety GL driver for our Nvidia FX1300 (see copy/paste below) and we're not running MESA. - although...we also have this freeglut (/usr/pymol/pymol.exe): unable to create... error (but i never saw this since i (also) created shortcuts (in gnome) to pymol - so the 'problem' is not fixed. And if i read the text below...maybe it's not possible to fix this. - anyway...pymol shows a strange behavior: very slow startup of the tcl/tk window (but that's probably a problem of redhat/gnome...while on a Suse/KDE system i don't see this) - and further, pymol always directly switches on the transmitter of the 3D stereo...although not showing or using stereo. - off topic: we bought this linux machine(s) to replace our old SGIs since Insight became available for Linux systems, saving ourselves a lot of money (SGIs are expensive). Thanks for the help. Best, Joris ./pymol freeglut (/usr/pymol/pymol.exe): Unable to create direct context rendering for w indow 'PyMOL Viewer' This may hurt performance. PyMOL(TM) Incentive Product - Copyright (C) 2006 DeLano Scientific LLC. A current PyMOL Maintenance and/or Support Subscription may be required for legal use of this Build beyond a finite honor-system evaluation period. Please visit http://www.pymol.org/funding.html for more information. This PyMOL Executable Build incorporates Open-Source PyMOL 0.99rc6. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: Quadro FX 1300/PCI/SSE2/3DNOW! GL_VERSION: 1.2 (2.0.2 NVIDIA 87.74) Hardware stereo capability detected. Adapting to Quadro hardware.
[PyMOL] Labeling CGO objects
Label gurus, I'm trying to label CGO objects with custom labels. I found the previous posts that explain how to create CGO text and then the painful way of reorienting the labels when the molecule is moved using cmd.rotate and cmd.translate. I'm curious if an easier way has been developed since the posts in 2002. I see that the distance command draws in CGO cylinders (dashes) between two atom selections and then labels them with the distance, meaning that it is possible in PyMOL to have labels tied to a CGO object. I've tried to generate a selection (since cmd.label requires a selection as the first param) from the CGO object but I don't think it's possible and cmd.label won't take my CGO object as the first param. I've succeeded in getting something close to what I want by labeling the closest atom to my CGO object with my custom label, and then translating the label using the mouse. But this procedure is not possible to do in a script or plugin. Is there a better way to label CGOs? Thanks for any ideas. -Ron Ron Jacak Graduate Student University of North Carolina - Chapel Hill
[PyMOL] dock one protein into another?
I'm having trouble figuring out how to use the edit mode in PyMol. I would like to dock an entire protein (a homodimer along with water) into another structure by rotating and translating manually. Is there a way to move multiple molecules like this as a group? Thanks Richard Gillilan MacCHESS
Re: [PyMOL] Labeling CGO objects
Ron, CGO labels are currently insufficient and need work. Right now, the only way to access high-quality labels (using scalable TrueType fonts) is to create fake atoms and then label them. Cheers, Warren PS. As a minor correction of fact, dashes aren't drawn with CGOs -- they're hard-coded at the C level as measurement objects. -- 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 -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Ron Jacak Sent: Monday, January 22, 2007 10:42 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Labeling CGO objects Label gurus, I'm trying to label CGO objects with custom labels. I found the previous posts that explain how to create CGO text and then the painful way of reorienting the labels when the molecule is moved using cmd.rotate and cmd.translate. I'm curious if an easier way has been developed since the posts in 2002. I see that the distance command draws in CGO cylinders (dashes) between two atom selections and then labels them with the distance, meaning that it is possible in PyMOL to have labels tied to a CGO object. I've tried to generate a selection (since cmd.label requires a selection as the first param) from the CGO object but I don't think it's possible and cmd.label won't take my CGO object as the first param. I've succeeded in getting something close to what I want by labeling the closest atom to my CGO object with my custom label, and then translating the label using the mouse. But this procedure is not possible to do in a script or plugin. Is there a better way to label CGOs? Thanks for any ideas. -Ron Ron Jacak Graduate Student University of North Carolina - Chapel Hill -- --- 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=sourceforge CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] dock one protein into another?
Richard, Probably the easiest way to do this is with the drag command. However, all of the atoms to be drag must be contained within a single molecular object. It is not currently possible to move multiple objects at once using the mouse. drag object-name Then move object with shift-(left or middle or right)-click-and-drag actions. Cheers, Warren -Original Message- From: pymol-users-boun...@lists.sourceforge.net [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Richard Gillilan Sent: Monday, January 22, 2007 1:48 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] dock one protein into another? I'm having trouble figuring out how to use the edit mode in PyMol. I would like to dock an entire protein (a homodimer along with water) into another structure by rotating and translating manually. Is there a way to move multiple molecules like this as a group? Thanks Richard Gillilan MacCHESS -- --- 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=sourceforge CID=DEVDEV ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
Re: [PyMOL] Labeling CGO objects
Hi Warren | CGO labels are currently insufficient and need work. Right now, the only | way to access high-quality labels (using scalable TrueType fonts) is to | create fake atoms and then label them. What's the recommended way to do this? Can you just put them anywhere you like, irrespective of any underlying physical model? And then presumably make them zero radius, or give them the background color, etc. so as not to see them? Terry
Re: [PyMOL] Labeling CGO objects
| CGO labels are currently insufficient and need work. Right now, the | only way to access high-quality labels (using scalable TrueType fonts) | is to create fake atoms and then label them. What's the recommended way to do this? Can you just put them anywhere you like, irrespective of any underlying physical model? Yes. The open-source code sponsor-only 1.x beta builds have a new pseudoatom command that makes this particularly convenient. pseudoatom my_lab, pos=[3.0,4.0,5.0], label=Custom Label Text You can even drag the label around with the mouse (ctrl-left-click drag). And then presumably make them zero radius, or give them the background color, etc. so as not to see them? No need -- simply: as label, object-name to hide any atomic representation. Cheers, Warren
