Re: [PyMOL] CONECT table

[Engin Ö. <eo...@uc...>]

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
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>> Direct: (604) 827-1122 | F: (604) 827-1299 | E: mh...@cd... |
>> www.cdrd.ca
>>
>>
>>
>>
>>
>>
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-- 
Engin Özkan, Ph.D.
Assistant Professor
Dept of Biochemistry and Molecular Biology
University of Chicago
Phone: (773) 834-5498
http://ozkan.uchicago.edu