Thanks, works beautifully!
Just FYI, it's not my structure, I was tasked with making a few pretty
pictures, that's all :)
Markus
From: Engin Özkan [mailto:eoz...@uchicago.edu]
Sent: Tuesday, October 07, 2014 7:35 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] CONECT table
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...@cowsandmilk.net]
Sent: Monday, October 06, 2014 4:40 PM
To: Markus Heller
Cc: pymol-users@lists.sourceforge.net<mailto: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><mailto: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
--
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NMR Scientist
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