Re: [PyMOL] Assign secondary structure on group
The latest update to SVN fixes this. Cheers, Thomas Thomas Holder wrote, On 03/06/15 15:35: Hi Matt, thanks for the bug report. If you use the command line instead, it works if you put the group name in parenthesis, which forces PyMOL to treat it as an atom selection: PyMOL dss (nameofgroup) Cheers, Thomas On 06 Mar 2015, at 14:53, Matthew Baumgartner mp...@pitt.edu wrote: Hi, I'm using pymol 1.7.4.0. The A assign sec. struct. command doesn't seem to work when you call it on a group. It works fine on the objects in the group individually, but it doesn't apply the command to the objects when called from a group. Thanks, Matt Baumgartner -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ 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] Assign secondary structure on group
Hi Matt, thanks for the bug report. If you use the command line instead, it works if you put the group name in parenthesis, which forces PyMOL to treat it as an atom selection: PyMOL dss (nameofgroup) Cheers, Thomas On 06 Mar 2015, at 14:53, Matthew Baumgartner mp...@pitt.edu wrote: Hi, I'm using pymol 1.7.4.0. The A assign sec. struct. command doesn't seem to work when you call it on a group. It works fine on the objects in the group individually, but it doesn't apply the command to the objects when called from a group. Thanks, Matt Baumgartner -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ 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] assign secondary structure?
* Michael Bovee mbo...@uvm.edu [2003-12-16 14:27] wrote: Hmm. When I try this I get a syntax error: __ PyMOLload EcHRSade.pdb Executive: object EcHRSade created. PyMOLhide PyMOLshow cartoon PyMOLdss EcHRSade Traceback (most recent call last): File /sw/lib/pymol/modules/pymol/parser.py, line 251, in parse exec(com2[nest]+\n,pymol_names,pymol_names) File string, line 1 dss EcHRSade ^ SyntaxError: invalid syntax _ I also get the error if I type on the command line dss EcHRSade.pdb Apparently pymol's dss works for others? Maybe a problem in the fink package, or on my particular system? I'm running the current fink package, 0.90-2, compiled from source on my PBG3(Lombard/Bronze). I think this is the problem. The dss command was introduced in version 0.91. I think you need to upgrade. Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
RE: [PyMOL] assign secondary structure?
Michael, Unfortunately PYMOL/dss doesn't generate quite enough information to recreate PDB SHEET and HELIX records. PyMOL (like other programs) simplifies the secondary structure concept down to a per-residue property. There is no such thing as a sheet or helix in PYMOL, but merely sets of proximal residues with a secondary structure property (ss) of 'H' or 'S'. load object-name.pdb hide show cartoon dss object-name Should be sufficient to get you a secondary structure representation for any protein. States represent multiple conformations -- you shouldn't need to worry about them Cheers, Warren -- mailto:war...@delanoscientific.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users- ad...@lists.sourceforge.net] On Behalf Of Michael Bovee Sent: Thursday, December 11, 2003 1:38 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] assign secondary structure? Hi, I have a 'raw' pdb file of atom coordinates only, and I'm hoping to use the dss command in pymol to get helix and strand designations that I can paste back into the header space of the pdb so that I can model fancy helices and strands and so forth to get a nice picture in pymol. Then I can superpose features with homologous proteins for which this header info is available. I just didnt want to modify or create this header info 'by hand' if I didn't have to... But, I can't get dss to work in pymol (even the refman warns that this algorithm has not been rigorously validated). The refman says USAGE is dss selection, state Does this mean I need to first make a selection that encompasses some part (or whole) of the molecule, or should this work on the entire pdb? I don't know what 'states' are so I just opted for '0' which is supposed to mean 'all states'. Thanks, --Michael Bovee --- This SF.net email is sponsored by: SF.net Giveback Program. Does SourceForge.net help you be more productive? Does it help you create better code? SHARE THE LOVE, and help us help YOU! Click Here: http://sourceforge.net/donate/ ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
