Re: [PyMOL] Rendering memory errors
Hi Stephan Lloyd Watkins, > I am no longer able to use the rendering plugin , which is a vlauble asset as > I am at this moment in the midst of making some publication quality figures. Which rendering plugin are you referring to? What type of computer are you using? > Additional, the standard ray trace option will only work if I use a white > background, and zoom out further than would make a good image, ie a 300 amino > protein about 1 inch square on an 8x8 inch window (visual field). How are you ray tracing? Using the 'ray' command? Clicking the 'ray' button? What happens if you do not use a white background? These bugs sound like they're related to the plugin, not PyMOL itself. Can you share your PyMOL session file with me? > As it is both the rendering types, I assume it is some change to memory > utilized by the shaders, as it crashes everytime. I have a similar problem > now with gimp as well, however the memory cap is easy to see and maxes out > around 3-4 G before crashing, however there is a 16 G memory, along with 4G > on the GPU so I do not know where the errors come from. I do not get the > errors on VMD, however prefer Pymol for the ease of use and also the images > are nice. If you have Intel-based hardware you might try the following settings upon startup: set use_shaders, 0 set sphere_mode, 0 and then try your rendering plugin. Cheers, -- Jason -- Jason Vertrees, PhD Director of Core Modeling Product Management Schrödinger, Inc. (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] Viewing PyMol in 3D
Hey everyone, Does anyone have experience setting up pymol to be viewed in 3D with glasses? I'm hoping to build a system for this purpose. >From what I have read, I will need a recent NVidia Quadro card and a >3D-capable LCD monitor with a resolution of at least 120Hz. I'm not sure if I >need to be more specific than that (if there are particular cards/monitors >that are known to work/not work). I'm also not quite sure if this is possible >on Windows 7. I've seen reports of people doing this with Windows XP and >Vista, but I would prefer to avoid those operating systems. Any suggestions or advice would be greatly appreciated. -Max F -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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] Viewing PyMol in 3D
Hi Max, you are already pretty much spot on. Pymol stereo works under XP, Vista, W7 and as far as I know any Linux flavor, as long as you purchase a compatible NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux you need to have a card which supports the external 3 pin stereo connector, you don't need that under any of the windows flavors. Check the Nivida website for compatible cards, machines and monitors. I'm sure you can also find some structural biology groups at Scripps who are already setup with this equipment. HTH Carsten From: Max Ferretti [mailto:mferr...@scripps.edu] Sent: Monday, December 10, 2012 11:22 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Viewing PyMol in 3D Hey everyone, Does anyone have experience setting up pymol to be viewed in 3D with glasses? I'm hoping to build a system for this purpose. >From what I have read, I will need a recent NVidia Quadro card and a >3D-capable LCD monitor with a resolution of at least 120Hz. I'm not sure if I >need to be more specific than that (if there are particular cards/monitors >that are known to work/not work). I'm also not quite sure if this is possible >on Windows 7. I've seen reports of people doing this with Windows XP and >Vista, but I would prefer to avoid those operating systems. Any suggestions or advice would be greatly appreciated. -Max F -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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] Shrinking the sidebar
Hi All, I was just wondering if it was possible to shrink the sidebar width so I have more viewing space? I regularly work with multiple windows open, usually splitscreen (vertically split). Since I do most of my work on a laptop with a 14-inch screen, that doesn't afford me much space to investigate my models with. I've tried dragging; it hasn't worked. Is there a a way to do it, or would the actual GUI source code have to be edited? Thanks, Alex -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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] Shrinking the sidebar
On Mon, Dec 10, 2012 at 12:02 PM, Alex Truong wrote: > I was just wondering if it was possible to shrink the sidebar width so I > have more viewing space? I regularly work with multiple windows open, > usually splitscreen (vertically split). Since I do most of my work on a > laptop with a 14-inch screen, that doesn't afford me much space to > investigate my models with. I've tried dragging; it hasn't worked. Is there > a a way to do it, or would the actual GUI source code have to be edited? Is this what you wanted? set internal_gui_width, 100 Or to really get rid of it: set internal_gui, 0 -Nat -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] Shrinking the sidebar
Sorry, I forgot the [PyMOL] subject header. On Mon, Dec 10, 2012 at 3:02 PM, Alex Truong wrote: > Hi All, > > I was just wondering if it was possible to shrink the sidebar width so I > have more viewing space? I regularly work with multiple windows open, > usually splitscreen (vertically split). Since I do most of my work on a > laptop with a 14-inch screen, that doesn't afford me much space to > investigate my models with. I've tried dragging; it hasn't worked. Is there > a a way to do it, or would the actual GUI source code have to be edited? > > Thanks, > Alex > -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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] Shrinking the sidebar
Alex, there is a little rectangle under the S of "State" in the lower left of the sidebar or to the left of the |< button. You can use that as a slider for the sidebar From: Alex Truong [mailto:atru...@bu.edu] Sent: Monday, December 10, 2012 3:03 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Shrinking the sidebar Hi All, I was just wondering if it was possible to shrink the sidebar width so I have more viewing space? I regularly work with multiple windows open, usually splitscreen (vertically split). Since I do most of my work on a laptop with a 14-inch screen, that doesn't afford me much space to investigate my models with. I've tried dragging; it hasn't worked. Is there a a way to do it, or would the actual GUI source code have to be edited? Thanks, Alex -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d___ 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] Viewing PyMol in 3D
You don't need a quadro with a 3 pin port to do stereo in linux anymore, but you do need a "new" model quadro, e.g. a quadro 600. The tradeoff is that you'll pay more for the 120hz monitors with the built-in 3d vision v2 emitters, see here : http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008177.html I haven't' tested a standalone 3d vision v2 emitter with linux, it may behave the same way as the lcd's with the built-in v2 emitter. > NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux > you need to have a card which supports the external 3 pin stereo connector, > you don’t need that under any of the windows flavors. Check the Nivida -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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] Viewing PyMol in 3D
Thanks Sabuj, useful info indeed. -Original Message- From: Sabuj Pattanayek [mailto:sab...@gmail.com] Sent: Monday, December 10, 2012 4:18 PM To: Schubert, Carsten [JRDUS] Cc: Max Ferretti; pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Viewing PyMol in 3D You don't need a quadro with a 3 pin port to do stereo in linux anymore, but you do need a "new" model quadro, e.g. a quadro 600. The tradeoff is that you'll pay more for the 120hz monitors with the built-in 3d vision v2 emitters, see here : http://plato.cgl.ucsf.edu/pipermail/chimera-users/2012-November/008177.html I haven't' tested a standalone 3d vision v2 emitter with linux, it may behave the same way as the lcd's with the built-in v2 emitter. > NVIDIA quadro card and Nvidia 3D kit. The only caveat is that under Linux > you need to have a card which supports the external 3 pin stereo connector, > you don't need that under any of the windows flavors. Check the Nivida -- LogMeIn Rescue: Anywhere, Anytime Remote support for IT. Free Trial Remotely access PCs and mobile devices and provide instant support Improve your efficiency, and focus on delivering more value-add services Discover what IT Professionals Know. Rescue delivers http://p.sf.net/sfu/logmein_12329d2d ___ 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
