Hi,
It appears that the following:
Select gluco, bound_to resn NDG
Show sticks, gluco
does not work. I'm not sure if the glycosylation is handled as a separate
residue, but you could try:
select glucoasp, byres (neighbor (resn NDG))
show sticks, glucoasp
FYI: There are pages on selection algebra on the Pymol wiki that may give
more inspiration.
Hope this gets you started,
/Andreas
On Oct 7, 2014 10:02 PM, "Markus Heller" <mhel...@cdrd.ca> 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...@cowsandmilk.net]
> Sent: Monday, October 06, 2014 4:40 PM
> To: Markus Heller
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] CONECT table
>
> http://www.pymolwiki.org/index.php/Connect_mode
>
> -David
>
> > On Oct 6, 2014, at 6:35 PM, Markus Heller <mhel...@cdrd.ca> 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: mhel...@cdrd.ca |
> > 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 (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
>
>
> ------------------------------------------------------------------------------
> 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 (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
>
------------------------------------------------------------------------------
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 (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
