[Chimera-users] Display only selection

Elaine Meng meng at cgl.ucsf.edu
Thu Jan 20 09:41:03 PST 2011

Hi Damien,
(1) selecting multiple residues from multiple chains.  There are several ways; here are a few:

(a) if using the mouse in the Sequence tool, first change the selection mode to "append" instead of "replace" (menu: Select... Selection Mode... append).  Then you don't have to use Shift, simply use the mouse to select multiple individual residues in the Sequence windows.  (even if you are in "replace" mode, Ctrl is not needed to select in the Sequence window)  After selecting the residues, however, you may want to change the selection mode back to "replace" to avoid later confusion.

(b) if you know the numbers you can just select with a command, e.g.: select :45.a,49.a,112.b,60.b 

(c) or you can select part of each residue in the main Chimera window, Ctrl-click the first and then Shift-Ctrl-click the others (or if you are in "append" mode, the Shift is not needed) then press keyboard up arrow or choose menu: Select.. Broaden if you want to promote the selection to the whole residues.

(2) showing only those residues. 
(a) atoms/bonds.  After selection, choose menu: Actions... Atoms/Bonds... show only, or use command: show sel
(or you could skip the selection step and use a command something like: show :45.a,49.a,112.b,60.b  )

(b) ribbons, surface etc.  The above only takes care of the atoms and bonds.  There still may be ribbons etc. shown for other residues.  After doing the selecting and showing of atoms, you could invert selection (several ways, one is to press keyboard right arrow) and then use the Actions menu to hide ribbons etc.

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 Jan 20, 2011, at 1:33 AM, Damien Larivière wrote:

> Dear Chimera team,
> I'm identifying a complex between two proteins thanks to crosslink data.
> I have the following questions:
> 1/ I would like to select two residues that belong to two different 
> chains and highlight them in the viewport.
> By using the sequence tool and then ctrl/shift+drag, I can select two 
> residues (ex: 45 and 246 of chain A), they are highlighted in the view. 
> But when I operate this way with res 45 of chain A and res 246 of chain 
> B, only one remains highlighted in the view port.
> One way to sort this out would have been to rename all the chains with 
> the letter A. But once the residues are highlighted, I have to measure 
> the distance between them, then to make one chain active and then to 
> move it and try to fit crosslink data (I hope I'm clear:-\ ).
> Is it possible to directly select and highlight in the viewport residues 
> of interest belonging to different chains?
> 2/ Supposing that I can select and highlight in the viewport residues of 
> interest belonging to different chains:
> How can I display only them in the viewport (and hide all the others)?
> The technical goal behind these questions is to better appreciate 
> visually the distance between residues of interest and, thanks to the 
> distance tool, to move one protein with respect to the other and fit 
> crosslink data.
> Many thanks for your help.
> Damien

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