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 -------------- 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
