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Re: [PyMOL] PyMOL on the Mac
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From: Tsjerk W. <ts...@gm...> - 2010-03-16 14:05:47
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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...@co...> 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 > <gre...@ro...> 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:ts...@gm...] >> Sent: Tuesday, March 16, 2010 6:17 AM >> To: Jason Vertrees >> Cc: pym...@li...; 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 >> <jas...@sc...> 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) Jas...@sc... >>> (o) +1 (603) 374-7120 >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® 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 (PyM...@li...) >>> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >>> Archives: http://www.mail-archive.com/pym...@li... >>> >> >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> Computational Chemist >> Medicinal Chemist >> Neuropharmacologist >> >> >> >> ------------------------------------------------------------------------------ >> Download Intel® 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 (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > > ------------------------------------------------------------------------------ > Download Intel® 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist |