[Chimera-users] Selecting just 1 carbohydrate chain

Elaine Meng meng at cgl.ucsf.edu
Thu Mar 12 11:07:56 PDT 2015

Hello Tein Foong Leong,
There are many ways to specify only a particular residue or chain.  You can see the residue number and chain ID of a residue by hovering the cursor over it and seeing the information that pops up.

(A) One way is by residue number and chain ID in the command line (show command line from the Favorites menu).  For example, command:

color red :15.C

… colors only residue number 15 in chain C.  

(B) Or, you might want to select the residue interactively in the Chimera window.  You can select an atom with Ctrl-click and then press keyboard up arrow to expand the selection (see green highlights) to the whole residue, or up arrow again to whole chain (or down arrow to go back down if you overshoot).  You can select an atom in one residue with Ctrl-click and then another atom in another residue with Shift-Ctrl-click…. then up arrow will expand to both of those whole residues.

(C ) Or, with select menu you could first select all carbohydrates and then deselect only the ones with a specific chain ID with either a command (for example, "~select :.B" would deselect chain B only) or the menu:

menu: Select… Selection Mode… subtract
menu: Select… Chain… B
menu: Select… Selection Mode… replace

(the latter to change the mode back to replace so that you don't get confused later by the subtraction mode)

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 12, 2015, at 7:34 AM, "Tein Leong (PG Research)" <t.f.leong at dundee.ac.uk> wrote:

> Hello,
> Thank you for the amazing programme. I’m using it for the first time and I can do most of the things I needed to do. I am writing to ask if it is possible to “color” just one carbohydrate chain ?
> I’m coloring an antibody crystal structure which is made up of two heavy chains. Each chain has a carbohydrate attached. I wanted to color both carbohydrate in different colors but I’m unable to do so. When I go to “Select” > “Residue” , the programme can only select all carbohydrate residues. Please advice.
> Thanks !
> Best wishes,
> Tein Foong Leong
> PhD Student
> Jacqui Wood Cancer Centre, Level 7
> Ninewells Hospital
> University of Dundee
> DD1 9SY

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