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
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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@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
On Apr 19, 2023, at 9:01 AM, Elaine Meng meng@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
participants (2)
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Coillie, Julie van -
Elaine Meng