Hi all, The "auto_show_classified" feature is now available from the open-source SVN code repository. I've also uploaded pre-compiled builds to http://pymol.org/download (alpha release, not intended for production use).
The setting has 3 modes: 0 (off, default), 1 (like Adam suggested), 2 (including the default lines), and 3 (simplified version with ribbon instead of cartoon). See also: http://pymolwiki.org/index.php/auto_show_classified Any feedback will be appreciated. Cheers, Thomas On 08 Feb 2016, at 15:16, H. Adam Steinberg <h.adam.steinb...@gmail.com> wrote: > Every application has to satisfy it's users. > > Thinking out loud… > If you show all lines the new users find it confusing and overwhelming but > they do get to see every atom. Experienced users generally know what atoms > are in a PDB or know how to find them if they are looking for them and > therefore do not need to see all lines. > > The current proposal is to show more structure (cartoon, sticks, spheres) but > leave on all lines behind this structure. My first thought is what would that > look like. So I open a current structure and show both options (attached). If > I leave all lines on it’s still a bit of a mess. I think it looks better with > all lines off. > > > > <Screen Shot 2016-02-08 at 2.13.53 PM.pdf><Screen Shot 2016-02-08 at 2.14.06 > PM.pdf> > > > >> On Feb 8, 2016, at 1:29 PM, Thomas Holder <thomas.hol...@schrodinger.com> >> wrote: >> >> 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 > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 -- 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. 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