Thanks for the info about the Pymol wiki page on Selection algebra. I looked at
it before, but I must have never gotten the proper syntax ☹
From: Andreas Warnecke [mailto:4ndreas.warne...@gmail.com]
Sent: Tuesday, October 07, 2014 4:26 PM
To: Markus Heller
Cc: David Hall; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] CONECT table
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<mailto: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<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
>
> --
> Markus Heller, Ph.D.
> NMR Scientist
> CDRD - The Centre for Drug Research and Development
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