[Chimera-users] select chain and elements simultaneously

Elaine Meng meng at cgl.ucsf.edu
Tue Dec 2 08:54:06 PST 2014


Hi folks,
What Boris suggests will probably work; it will select atoms in chain A with 1-, 2- or 3-letter names starting with C.

However, the most direct way (in a command) to specify carbons in chain A would be to intersect chain A with element symbol C, e.g.:

color red :.A & C

The first part is the chain specifier, the & means intersection, and the last part is the element symbol, which is one of the built-in classifications, see the command-line atomspec docs:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

Also, consider whether you want to color atoms/bonds, ribbons, surface, etc.  To color atoms only (not the ribbon etc.), the command would be something like:

color red,a :.A & C

Above I only mentioned commands.  You could do the same thing with the menu, but it would be more steps:

Select… Chain… A
Select… Selection Mode… intersect
Select… Chemistry… element… C
Actions… Color… red  (or Actions… Color… all options, set coloring target for example to atoms/bonds only, then choose color)

Then you would probably want to change the selection mode back to replace and the coloring target back to all of the above to avoid later confusion.

Best,
Elaine
----------
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 1, 2014, at 5:25 PM, Boris Steipe <boris.steipe at utoronto.ca> wrote:

> I think ...
> 
>  select :*.A at C@C?@C??
> 
> ... will do that. This is:
> : - for all models
> *.A - for all residues in chain A
> @C  - select C
> @C? - also select C plus one wildcard (CB, CG ...
> @C?? - also select C plus two wildcards (CG1, CD2 ...) 
> 
> cf. https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
> 
> Cheers,
> B.
> 
> On Dec 1, 2014, at 6:25 PM, Jacob Lewis <jacoblewis90 at gmail.com> wrote:
> 
>> Hi all, 
>> 
>> I am new to chimera is it possible to select chain and element for a structure? for instance select chain A and element carbons so they can be coloured red for example? 
>> 
>> thanks in advance. 
>> 
>> Jacob  
>> 




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