Since version 1.8.2, PyMOL auto-detects CA-only models, so no ribbon_trace_atoms or cartoon_trace_atoms needed anymore.
A nice tool that can assign secondary structure with CA trace only is SST: http://lcb.infotech.monash.edu.au/sstweb2/ PSICO has an SST wrapper, so you can run it directly in PyMOL: run https://raw.githubusercontent.com/speleo3/pymol-psico/master/psico/editing.py fetch 3b5d, async=0 sst show cartoon Hope that helps. Cheers, Thomas On 02 Dec 2016, at 08:24, Spencer Bliven <spencer.bli...@gmail.com> wrote: > There is a cartoon variant too, although everything will look like a loop > > set cartoon_trace_atoms, on > show cartoon, polymer > > On Wed, Oct 26, 2016 at 12:27 AM, Yuxing Liao > <yuxing.l...@utsouthwestern.edu> wrote: > Hi Mohsen, > > The PDB file of 3B5D only contains CA atoms, so most rendering like cartoon > fails. You could try to visualize it by "set ribbon_trace_atoms, 1" and then > show it as ribbon. > > Yuxing > > -----Original Message----- > From: pymol-users-requ...@lists.sourceforge.net > [mailto:pymol-users-requ...@lists.sourceforge.net] > Sent: Tuesday, October 25, 2016 4:50 PM > To: pymol-users@lists.sourceforge.net > Subject: PyMOL-users Digest, Vol 125, Issue 14 > > Send PyMOL-users mailing list submissions to > pymol-users@lists.sourceforge.net > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/pymol-users > or, via email, send a message with subject or body 'help' to > pymol-users-requ...@lists.sourceforge.net > > You can reach the person managing the list at > pymol-users-ow...@lists.sourceforge.net > > When replying, please edit your Subject line so it is more specific than "Re: > Contents of PyMOL-users digest..." > > ------------------------------ > > Message: 4 > Date: Tue, 25 Oct 2016 21:34:01 +0000 > From: Mohsen Chitsaz <mohsen.chit...@flinders.edu.au> > Subject: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol > To: "pymol-users@lists.sourceforge.net" > <pymol-users@lists.sourceforge.net> > Message-ID: > > <sg2pr03mb15688f28895fd8bf7a322112d5...@sg2pr03mb1568.apcprd03.prod.outlook.com> > > Content-Type: text/plain; charset="us-ascii" > > Hi everyone, > > Can someone please assist me opening this pdb file? I am trying to open EmrE > protein (pdb: 3B5D) in Pymol a and show it as cartoon representation, but it > opens up as many little cross signs seem to be corresponding to CA atoms. > When I try to preset it pretty or any other preset options, it disappears. > The command "show cartoon" is not doing anything on it. > > Cheers > Mohsen > > ________________________________ > > UT Southwestern > > Medical Center > > The future of medicine, today. -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ 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
