Oh, and it should be glucoasn, of course. :-P
On Oct 8, 2014 1:26 AM, "Andreas Warnecke" <4ndreas.warne...@gmail.com>
wrote:
> 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
>> >
>> >
>> >
>> >
>> >
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