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 >> >> ________________________________ >> >> CONFIDENTIAL TRANSMISSION - This message, including any attachments, is >>confidential and may be privileged. If you are not the intended >>recipient, please delete it without further distribution and reply to >>the sender that you have received the message in error. >> >> >>------------------------------------------------------------------------- >>----- >> 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 > >H. Adam Steinberg >7904 Bowman Rd >Lodi, WI 53555 >608/592-2366 > > >-------------------------------------------------------------------------- >---- >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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