[Chimera-users] selecting by radius

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 4 09:34:10 PST 2010

You can select using a radius or "zone" around some central atoms:

(1) Select the central atoms.  For example, you could select one amino  
acid by Ctrl-clicking on one of its atoms and then pressing the  
keyboard up arrow key.  Another way to select one amino acid is to  
show Sequence (under Favorites menu) and choose it from the sequence  

(2) Choose "Select... Zone" from the menu, enter desired radius value,  
and turn on "Select all atoms/bonds of any residue in selection zone"  
if you want to select whole residues instead of parts of residues,  
click OK.

(3) then do something to your selection, for example hide everything  
else by choosing "Actions... Atoms/Bonds... show only" from the menu.   
That only affects atom/bond display.  If you have other stuff like  
ribbons and surfaces you will need to hide those separately, which can  
also be done with the Actions menu.  Ribbons/surfaces don't have "show  
only" but you can use "Select... Invert Selection" first and then hide  
those parts, or "Select... Clear Selection" first to just hide all  

You can also select zones with commands.  For example, to select  
residues within 4.5 angstroms of residue 12 in chain A:

sel :12.a z<4.5

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 Dec 27, 2009, at 8:21 AM, gytjyb wrote:
> I still thank for you!
> Maybe, I should learn some basic knowlenge!
> Do you tell me how to hide all parts except for selected animo acid  
> by redias?

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