[chimerax-users] Unable to select individual glycans in ChimeraX

[Elaine Meng]

Dear Julie,
You can Ctrl-click on an atom in the 3D view to select it, and then press keyboard up arrow to promote the selection to the whole residue.  Maybe that will suffice for what you want to do.  

Alternatively (or in addition) you can label all the glycosylation residues, e.g.

open 7cn9
label :bma,fuc,man,nag height 2

... which will show their residue names and numbers.  I can also see from the log that this structure contains 3 copies of the same sequence as chains A,B,C.  You can use the chain IDs and residue numbers in selection commands, or just bypass selection and act directly with commands, e.g.

select :1205
... will select NAG 1205 in each of 3 chains, A, B, and C
select /A:1205
... will select NAG 1205 in chain A only
select /A:1-3
... will select the glycosylation group NAG 1, NAG 2, and BMA 3 in chain A
color /A,B:1202 magenta
... will color NAG 1202 in chains A and B magenta

See command-line specification:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/atomspec.html>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Apr 19, 2023, at 8:30 AM, Coillie, Julie van via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Dear ChimeraX,
> 
> Is there any way to select one individual glycan on a crystal structure?
> 
> The crystal structures I'm working with have multiple domains, each with glycans. I want to annotate the glycan per domain (every domain & glycan in a specific color). However, I can't edit individual glycan structures. The glycans are grouped under Non-standard residues, e.g. MAN, NAG, ... However, when selecting e.g. MAN, all the MAN structures light up, which are found on all 3 domains. 
> An alternative would be using the sequence and annotating each individual sugar by using "select". However, these Non-standard residues are not in the sequence (they are when uploading this in Pymol), so I don't know a position to select them on. Is there a way to find the "sequence" for non-standard residues or any other way to annotate an individual glycan.
> 
> Thank you in advance,
> Julie Van Coillie