Re: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
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 + > 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
Re: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
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: > <SG2PR03MB15688F28895FD8BF7A322112D5A80@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 > > -- next part -- > An HTML attachment was scrubbed... > > -- > > > -- > The Command Line: Reinvented for Modern Developers Did the resurgence of > CLI tooling catch you by surprise? > Reconnect with the command line and become more productive. > Learn the new .NET and ASP.NET CLI. Get your free copy! > http://sdm.link/telerik > > -- > > ___ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > End of PyMOL-users Digest, Vol 125, Issue 14 > > > > > UT Southwestern > > > Medical Center > > > > The future of medicine, today. > > > > > -- > The Command Line: Reinvented for Modern Developers > Did the resurgence of CLI tooling catch you by surprise? > Reconnect with the command line and become more productive. > Learn the new .NET and ASP.NET CLI. Get your free copy! > http://sdm.link/telerik > ___ > 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 > -- 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
[PyMOL] PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
PDB entry 3B5D is a low resolution (3.8 Å) structure that contains only C alpha coordinates (chain trace, no side chains) in the original pdb file. There are servers that will generate full backbone and side chain coordinates, e.g. SABBAC (http://bioserv.rpbs.univ-paris-diderot.fr/services/SABBAC/), however, be aware that low resolution structures do not get more precise by modelling in parts that were not resolved in the experimental structure . Annemarie Honegger Message: 4 Date: Tue, 25 Oct 2016 21:34:01 + 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 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik___ 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
Re: [PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
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 + 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 -- next part -- An HTML attachment was scrubbed... -- -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik -- ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users End of PyMOL-users Digest, Vol 125, Issue 14 UT Southwestern Medical Center The future of medicine, today. -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik ___ 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
[PyMOL] difficulty opening EmrE protein (pdb: 3B5D) in Pymol
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 -- The Command Line: Reinvented for Modern Developers Did the resurgence of CLI tooling catch you by surprise? Reconnect with the command line and become more productive. Learn the new .NET and ASP.NET CLI. Get your free copy! http://sdm.link/telerik___ 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
