[Chimera-users] select by residue type or category

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 19 11:45:32 PDT 2013

Hi Francesco,
You could either just select by residue type and chain ID, for example command

select :asp.j,glu.j

... or by amino acid category, for example command

select :.j & hydrophobic

see command-line atom specification (amino acid category is one of the built-in classifications):

These same things can be done with the Actions... Select menu, see submenus "Selection Mode... append" (allows building up a selection instead of always replacing it, or intersecting, as with a specific chain), "Chain...[chain ID]", "Residue... amino acid category" and/or "Residue... [residue name]" but the menu approach is more tedious/longer than commands.

The amino acid categories have default assignments taken from a literature reference as shown here,
... but you can change the assignments as you like using the ResProp tool, in menu under Tools... Structure Analysis.

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 19, 2013, at 11:17 AM, Francesco Malatesta wrote:

> Hello
> I would like to ask a simple question on selection. In the GroEL-GroES complex (pdb 1aon) how do you select, for example, hydrophobic or acidic residues or both  in the say  J chain?
> thank you very much
> Francesco Malatesta

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