Re: [PyMOL] Pymol error in Mac OS X 10.8.2
what method did you use for installation? -- David Hall On Wednesday, May 1, 2013 at 11:53 AM, Rhitankar Pal wrote: I am having some issues after installing pymol in Mac OS 10.8.2. It seems the program is installed but when I try to open in using command line pymol it doesn't show the 'Molecular Graphics System' window but shows only the 'Pymol Viewer' window. In the terminal I have the following error message: Detected OpenGL version 2.0 or greater. Shaders available. Detected GLSL version 1.20. OpenGL graphics engine: GL_VENDOR: NVIDIA Corporation GL_RENDERER: NVIDIA GeForce GT 640M OpenGL Engine GL_VERSION: 2.1 NVIDIA-8.10.44 304.10.65f03 Traceback (most recent call last): File /Library/Python/2.7/site-packages/pymol/__init__.py, line 450, in launch_gui __import__(self.invocation.options.gui) File /Library/Python/2.7/site-packages/pmg_tk/__init__.py, line 22, in module from PMGApp import * File /Library/Python/2.7/site-packages/pmg_tk/PMGApp.py, line 33, in module class PMGApp(Pmw.MegaWidget): File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py, - Ignored: line 131, in __getattr__ self._initialise() File /Library/Python/2.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwLoader.py, line 89, in _initialise raise ImportError(msg) ImportError: No module named tkinter Detected 4 CPU cores. Enabled multithreaded rendering. Any help to resolve this issue would be greatly appreciated. Thanks Rhitankar -- Rhitankar Pal Postdoctoral Researcher, Dept of Chemistry, Yale University New Haven, CT 06511 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net (mailto: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 -- Introducing AppDynamics Lite, a free troubleshooting tool for Java/.NET Get 100% visibility into your production application - at no cost. Code-level diagnostics for performance bottlenecks with 2% overhead Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap1 ___ 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] PyMOL on the Mac
I second Tsjerk on this, maybe in the .pymolrc? And auto_show_sticks would be very useful to me! Cheers, Greg -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Tuesday, March 16, 2010 6:17 AM To: Jason Vertrees Cc: pymol-users@lists.sourceforge.net; David Hall Subject: Re: [PyMOL] PyMOL on the Mac Hi Jason, Along those lines, would it be possible to have a 'default' which can be set to a list of settings related to appearance? That might be more concise than to have everything in a separate setting. set default,[cartoon, lines, nonbonded, cbaw] The default value as pymol starts up now would be [lines, nonbonded, cbag]. Just my 2 eurocents... Cheers, Tsjerk On Tue, Mar 16, 2010 at 12:53 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: David, You may remember writing: A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Well, reading through the source today, I found a couple settings that few know about--and I might add more similar settings: auto_show_lines == show a newly loaded object with lines representation? auto_show_spheres == show a newly loaded object with spheres representation? auto_show_nonbonded == show newly loaded non-bonded? If these are considered useful, I can add others like: auto_show_cartoon(s) # example set auto_show_spheres fetch 1cll This offers some more flexibility for the user to choose lines or other default representation. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] PyMOL on the Mac
I think if Jason provides a full complement of auto_show_* for the representations, this should be partially possible without an additional setting. By default, pymol seems to have these settings: auto_show_lines=on auto_show_nonbonded=on auto_show_spheres=off Some quick testing of changing these settings by putting lines in my .pymolrc shows that I can instead have only spheres be shown in the file I'm opening with pymol by doing: set auto_show_lines, off set auto_show_nonbonded, offf set auto_show_spheres What is missing is the ability to have a default coloring. Is that possible? The auto_color setting is already taken for whether or not pymol loops through the list of colors in layer1/Color.c ... What might be interesting is a callback that could be run on an object whenever a user loads a file. Then you can do whatever you wanted. -David On Tue, Mar 16, 2010 at 3:45 AM, Gerebtzoff, Gregori gregori.gerebtz...@roche.com wrote: I second Tsjerk on this, maybe in the .pymolrc? And auto_show_sticks would be very useful to me! Cheers, Greg -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Tuesday, March 16, 2010 6:17 AM To: Jason Vertrees Cc: pymol-users@lists.sourceforge.net; David Hall Subject: Re: [PyMOL] PyMOL on the Mac Hi Jason, Along those lines, would it be possible to have a 'default' which can be set to a list of settings related to appearance? That might be more concise than to have everything in a separate setting. set default,[cartoon, lines, nonbonded, cbaw] The default value as pymol starts up now would be [lines, nonbonded, cbag]. Just my 2 eurocents... Cheers, Tsjerk On Tue, Mar 16, 2010 at 12:53 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: David, You may remember writing: A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Well, reading through the source today, I found a couple settings that few know about--and I might add more similar settings: auto_show_lines == show a newly loaded object with lines representation? auto_show_spheres == show a newly loaded object with spheres representation? auto_show_nonbonded == show newly loaded non-bonded? If these are considered useful, I can add others like: auto_show_cartoon(s) # example set auto_show_spheres fetch 1cll This offers some more flexibility for the user to choose lines or other default representation. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https
Re: [PyMOL] PyMOL on the Mac
Hi David, Yes, my point was also for keeping it a bit concise. There's so many settings already... If everything gets 'fully complemented' people are less likely to find what they're looking for. In this regard, it is already illustrating that Jason replied Well, reading through the source today, I found a couple settings that few know about. From the statement it seems that 'few' was already Jason-exclusive :p Cheers, Tsjerk On Tue, Mar 16, 2010 at 2:26 PM, David Hall li...@cowsandmilk.net wrote: I think if Jason provides a full complement of auto_show_* for the representations, this should be partially possible without an additional setting. By default, pymol seems to have these settings: auto_show_lines=on auto_show_nonbonded=on auto_show_spheres=off Some quick testing of changing these settings by putting lines in my .pymolrc shows that I can instead have only spheres be shown in the file I'm opening with pymol by doing: set auto_show_lines, off set auto_show_nonbonded, offf set auto_show_spheres What is missing is the ability to have a default coloring. Is that possible? The auto_color setting is already taken for whether or not pymol loops through the list of colors in layer1/Color.c ... What might be interesting is a callback that could be run on an object whenever a user loads a file. Then you can do whatever you wanted. -David On Tue, Mar 16, 2010 at 3:45 AM, Gerebtzoff, Gregori gregori.gerebtz...@roche.com wrote: I second Tsjerk on this, maybe in the .pymolrc? And auto_show_sticks would be very useful to me! Cheers, Greg -Original Message- From: Tsjerk Wassenaar [mailto:tsje...@gmail.com] Sent: Tuesday, March 16, 2010 6:17 AM To: Jason Vertrees Cc: pymol-users@lists.sourceforge.net; David Hall Subject: Re: [PyMOL] PyMOL on the Mac Hi Jason, Along those lines, would it be possible to have a 'default' which can be set to a list of settings related to appearance? That might be more concise than to have everything in a separate setting. set default,[cartoon, lines, nonbonded, cbaw] The default value as pymol starts up now would be [lines, nonbonded, cbag]. Just my 2 eurocents... Cheers, Tsjerk On Tue, Mar 16, 2010 at 12:53 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: David, You may remember writing: A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Well, reading through the source today, I found a couple settings that few know about--and I might add more similar settings: auto_show_lines == show a newly loaded object with lines representation? auto_show_spheres == show a newly loaded object with spheres representation? auto_show_nonbonded == show newly loaded non-bonded? If these are considered useful, I can add others like: auto_show_cartoon(s) # example set auto_show_spheres fetch 1cll This offers some more flexibility for the user to choose lines or other default representation. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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
Re: [PyMOL] PyMOL on the Mac
These settings affect the atomistic representations upon instantiation. So, keeping it simple and very fast is best. I might add a few more settings along these lines, but I don't think I'm going to make it totally generic. Here's another reason why I love PyMOL: 5 minutes of coding gets you a personalized solution to this problem. Just change cartoon to whatever representation you want, or add other intermediate commands. Here's the code: # visLoad -- simple load wrapper that enables your desired visualization # # save this to a file called visLoad.py and then run that file # run /path/to/visLoad.py. visLoad will now be defined for # you in PyMOL. # import string import os from os import path def visLoad(filename, object=None, *args, **kwargs): if object==None: object = string.split(os.path.basename(filename),.)[0] cmd.set(suspend_updates) try: cmd.load(filename, object, *args, **kwargs) cmd.show_as(cartoon, object) finally: cmd.set(suspend_updates, off) cmd.extend(visLoad, visLoad) Cheers, -- Jason On Tue, Mar 16, 2010 at 1:16 AM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Jason, Along those lines, would it be possible to have a 'default' which can be set to a list of settings related to appearance? That might be more concise than to have everything in a separate setting. set default,[cartoon, lines, nonbonded, cbaw] The default value as pymol starts up now would be [lines, nonbonded, cbag]. Just my 2 eurocents... Cheers, Tsjerk On Tue, Mar 16, 2010 at 12:53 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: David, You may remember writing: A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Well, reading through the source today, I found a couple settings that few know about--and I might add more similar settings: auto_show_lines == show a newly loaded object with lines representation? auto_show_spheres == show a newly loaded object with spheres representation? auto_show_nonbonded == show newly loaded non-bonded? If these are considered useful, I can add others like: auto_show_cartoon(s) # example set auto_show_spheres fetch 1cll This offers some more flexibility for the user to choose lines or other default representation. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] PyMOL on the Mac
I would be a fan of auto_show_cartoon. Also, if you set more than one of these, it will auto show more th one representation. Coolness. If anyone is curious, I just figured out what auto_show_selections appears to do (it is on by default), so I'll try to document that tomorrow. Thanks, -David On Mar 15, 2010, at 7:53 PM, Jason Vertrees jason.vertr...@schrodinger.com wrote: David, You may remember writing: A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Well, reading through the source today, I found a couple settings that few know about--and I might add more similar settings: auto_show_lines == show a newly loaded object with lines representation? auto_show_spheres == show a newly loaded object with spheres representation? auto_show_nonbonded == show newly loaded non-bonded? If these are considered useful, I can add others like: auto_show_cartoon(s) # example set auto_show_spheres fetch 1cll This offers some more flexibility for the user to choose lines or other default representation. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] PyMOL on the Mac
David, You may remember writing: A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Well, reading through the source today, I found a couple settings that few know about--and I might add more similar settings: auto_show_lines == show a newly loaded object with lines representation? auto_show_spheres == show a newly loaded object with spheres representation? auto_show_nonbonded == show newly loaded non-bonded? If these are considered useful, I can add others like: auto_show_cartoon(s) # example set auto_show_spheres fetch 1cll This offers some more flexibility for the user to choose lines or other default representation. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] PyMOL on the Mac
Hi Jason, Along those lines, would it be possible to have a 'default' which can be set to a list of settings related to appearance? That might be more concise than to have everything in a separate setting. set default,[cartoon, lines, nonbonded, cbaw] The default value as pymol starts up now would be [lines, nonbonded, cbag]. Just my 2 eurocents... Cheers, Tsjerk On Tue, Mar 16, 2010 at 12:53 AM, Jason Vertrees jason.vertr...@schrodinger.com wrote: David, You may remember writing: A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Well, reading through the source today, I found a couple settings that few know about--and I might add more similar settings: auto_show_lines == show a newly loaded object with lines representation? auto_show_spheres == show a newly loaded object with spheres representation? auto_show_nonbonded == show newly loaded non-bonded? If these are considered useful, I can add others like: auto_show_cartoon(s) # example set auto_show_spheres fetch 1cll This offers some more flexibility for the user to choose lines or other default representation. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ 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] PyMOL on the Mac
On 20 Jan 2010, at 22:07, Jason Vertrees wrote: PyMOLers, I just want to quickly reiterate: PyMOL will still be supported on the Mac--no need to worry. Even though other Schrodinger software doesn't run on the Mac, PyMOL will. Actually, I expect that schrodinger will port their own software to the Mac sooner than later.-- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev___ 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] PyMOL on the Mac
Alright, here's a feature request that might convince people who still don't believe, despite your first commit to pymol trunk post-acquisition including Fixed a GL build bug on OSX (see http://pymol.svn.sourceforge.net/viewvc/pymol?view=revrevision=3887 ) A Pymol Quicklook plugin. My primary purpose would be for pses, but you might as well pick up pdbs and other formats supported by pymol along the way. For pdb files, I wouldn't want the default pymol view of lines colored by atom with green carbons being what I quicklook to, so either reading .pymolrc to get a default view or some variant ( .pymolqlrc ?) would be nice to allow users to customize their views. Also, maybe default to a cartoon representation colored by chains with het atoms as sticks and metals as spheres, but that's probably just forcing the view I want on others when I could just stick that in my personal .pymolqlrc type file. Hopefully I'm out of ideas nows, David - Original Message From: Jason Vertrees jason.vertr...@schrodinger.com To: pymol-users@lists.sourceforge.net Sent: Wed, January 20, 2010 4:07:45 PM Subject: [PyMOL] PyMOL on the Mac PyMOLers, I just want to quickly reiterate: PyMOL will still be supported on the Mac--no need to worry. Even though other Schrodinger software doesn't run on the Mac, PyMOL will. MacPyMOL will live on. Best, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ 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 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ 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
