Adam, Abhinav, Dave, thanks for the very useful feedback. To keep it simple, I propose a "auto_show_classified" setting (will depend on "auto_classify_atoms", on by default) which will be equivalent to:
show cartoon, polymer show sticks, organic show spheres, inorganic Question: should this automatically hide lines for classified atoms? By the way, you may also like the "nice" preset (with "x" alias) from psico: https://github.com/speleo3/pymol-psico/blob/master/psico/viewing.py Cheers, Thomas On 08 Feb 2016, at 13:50, Bourgaize David <dbourga...@whittier.edu> wrote: > My thoughts exactly! > > Dave Bourgaize > > On 2/8/16, 9:54 AM, "H. Adam Steinberg" <h.adam.steinb...@gmail.com> wrote: > >> Every year I teach students PyMOL, and the look on their faces when they >> first open a pdb in PyMOL and get a cluster of green sticksŠ yikes! >> >> YES!!! to the default being secondary structure, ligands as sticks, and >> metal ions as spheres! Add - nucleic acids as cartoon. >> >>> On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav <aku...@intrexon.com> wrote: >>> >>> Showing metal ions (and FES clusters etc) as spheres would also be >>> useful. >>> >>> Thanks, >>> Abhinav >>> >>> Abhinav Kumar, PhD >>> Senior Scientist, Bioinformatics >>> Intrexon, Inc. >>> 329 Oyster Point Blvd., South San Francisco, CA 94080 >>> (650) 597-4072 | aku...@intrexon.com >>> >>> >>> ________________________________________ >>> From: Thomas Holder [thomas.hol...@schrodinger.com] >>> Sent: Monday, February 08, 2016 8:51 AM >>> To: Ivan Vulovic; Schubert, Carsten [JRDUS] >>> Cc: pymol-users@lists.sourceforge.net >>> Subject: Re: [PyMOL] auto_show_cartoon or similar >>> >>> Hi Ivan and Carsten, >>> >>> I can take "auto_show_cartoon" as a feature request. It's trivial to >>> implement. >>> >>> What also would be nice: automatically showing sticks for ligands. e.g. >>> corresponding to the "not polymer" or the "organic" selection. Thoughts? >>> >>> Cheers, >>> Thomas >>> >>> On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS] >>> <cschu...@its.jnj.com> wrote: >>> >>>> Hi Ivan, >>>> >>>> you could either try to overload the ³load² function in Pymol (not >>>> sure this is supported) or write your own custom load function under a >>>> different name, which loads the protein, assigns the name of the >>>> object, hides lines and shows the cartoon. >>>> >>>> Sorry, this is a rather generic answer but should point you in the >>>> right direction. >>>> >>>> Cheers, >>>> >>>> Carsten >>>> >>>> From: Ivan Vulovic [mailto:i...@uw.edu] >>>> Sent: Saturday, February 06, 2016 8:18 PM >>>> To: pymol-users@lists.sourceforge.net >>>> Subject: [PyMOL] auto_show_cartoon or similar >>>> >>>> Hello >>>> >>>> Is there a way to make cartoon the default representation, something >>>> akin to "auto_show_lines", but for cartoon? There was some dicussion of >>>> this in 2010 (link below) but I haven't found anything more recent that >>>> does what I'd like. >>>> >>>> >>>> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734 >>>> .html >>>> >>>> Thanks >>>> Ivan -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Site24x7 APM Insight: Get Deep Visibility into Application Performance APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month Monitor end-to-end web transactions and take corrective actions now Troubleshoot faster and improve end-user experience. Signup Now! http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 _______________________________________________ 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
