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

[Elaine Meng]

> On Apr 19, 2023, at 9:01 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> select /A:1-3
> ... will select the glycosylation group NAG 1, NAG 2, and BMA 3 in chain A

One correction, that command doesn't do anything on the specific example structure 7cn9 because those residues aren't in chain A.  They are in chain V instead:

select /V:1-3

When there is more than one sugar residue in a glycosylation group, they get a different chain ID, but unfortunately only the peptide chains are listed in the Log and Select menu.

To figure out these other chain IDs, you would need to hover the mouse over the residue and see the pop-up information, and/or change the labels so that they also show the chain ID, e.g. 

select :bma,fuc,man,nag

...and use menu: Actions... Label... Residues... Chain, Name, Number

(probably also want to use Actions... Label... Set Label Height)

or if you needed to do it in a command, could be something like the following.  Personally, I like to put chain ID last to make it easier to see:

label :bma,fuc,man,nag height 2 text "{0.name} {0.number} {0.chain_id}"

I hope this helps,
Elaine