|
From: Engin Ö. <eo...@uc...> - 2014-10-08 02:35:08
|
fetch /<PDB/> hide everything show cartoon, all select NlinkedGlyco, resn NAG+BMA+MAN+FUC or byres (polymer within 2.0 of resn NAG+BMA+MAN+FUC) show sticks, NlinkedGlyco hide sticks, name C+CO+N This should do. Also, are you sure about NDG? If you are talking about N-linked glycosylation, as far as I know, there are no NDG (alpha monomer of N-actyl-D-glucosamine) in glycoproteins. NDG in N-linked sugars is usually an incorrectly modeled NAG (beta-N-acetyl-D-glucosamine), and the PDB is replete with this mistake (about a third of N-linked sugars are incorrectly named/modeled according to a paper by Thomas Lütteke). If this is your structure, I suggest you correct it. If you have to have NDG (because of an incorrect existing file from PDB), then add NDG to the two places I have common monomer names for sugars. Also, add galactose and sialic acid to that list; I don't remember their three-letter codes of the top of my head. Engin On 10/7/14 2:43 PM, Markus Heller wrote: > D'uh. Thanks for pointing this out. > > Follow-up question: I want to show my glycosylated protein as cartoon, with the glycosides *and* the side chains they're attached to shown in sticks. How do I do that? > > I show the protein as cartoon: > > Load foo.pdb > Hide lines > As cartoon > > Then I select the glycosides > > Select gluco, resn NDG > Show sticks, gluco > > This only shows me the glycoside, but NOT the side chain it's attached to. > > I tried > > Select gluco, bound_to resn NDG > Show sticks, gluco > > But that doesn't work, shows no side chains. > > Any help much appreciated! > > Thanks and Cheers > Markus > > -----Original Message----- > From: David Hall [mailto:li...@co...] > Sent: Monday, October 06, 2014 4:40 PM > To: Markus Heller > Cc: pym...@li... > Subject: Re: [PyMOL] CONECT table > > http://www.pymolwiki.org/index.php/Connect_mode > > -David > >> On Oct 6, 2014, at 6:35 PM, Markus Heller <mh...@cd...> wrote: >> >> Hello, >> >> How can I get PYMOL to use the CONECT table from a PDB file? My protein is glycosylated, and I'd like to properly and automatically display the glycosides including their linkage to the protein. >> >> Thanks and Cheers >> Markus >> >> -- >> Markus Heller, Ph.D. >> NMR Scientist >> CDRD - The Centre for Drug Research and Development >> 2405 Wesbrook Mall, Fourth Floor | Vancouver, BC V6T 1Z3 | Main: >> (604) 827-1147 >> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mh...@cd... | >> www.cdrd.ca >> >> >> >> >> >> >> Follow us: >> >> This email and any files transmitted with it are confidential and intended solely for the addressee. If you are not the named addressee you should not disseminate, distribute, copy, or alter this email. >> >> >> >> >> ---------------------------------------------------------------------- >> -------- Slashdot TV. Videos for Nerds. Stuff that Matters. >> http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg. >> clktrk _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: >> http://www.mail-archive.com/pym...@li... > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... -- Engin Özkan, Ph.D. Assistant Professor Dept of Biochemistry and Molecular Biology University of Chicago Phone: (773) 834-5498 http://ozkan.uchicago.edu |