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 sticks… 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 “load” 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. 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
