[Chimera-users] selecting

[Elaine Meng]

On Jan 17, 2005, at 7:52 AM, John Nixon wrote:
> I'm a newbie and am having trouble getting started.  Sorry to be dense.
>  
> Using the command line on a single protein chain O
>  
> select  :32-42,44-49.O
>  
> or
>   
> rep sphere  :43:56:59:60:61:63:65:67:68:70:71:72:73:74:75:78:110:113.0
>  
> only seems to work on the last residue.  Thus  I'd have to write a  
> separate command for each residue.
>  
> Could you tell me what I've missed please!

   Hi John,
Don't worry, this was almost right!  You can think of the chain ID
as part of the residue specification, so that you need to put it
on each residue number or range of residue numbers:

select :32-42.o,44-49.o

rep sphere  
:43.o:56.o:59.o:60.o:61.o:63.o:65.o:67.o:68.o:70-75.o:78.o:110.o:113.o

which is somewhat more of a pain to type, unfortunately.  The reason is  
that
theoretically there could be another chain that doesn't have an ID, so  
residue
numbers not together with a specification of chain O would specify  
residues
in the no-ID chain.

There are a few more examples in

http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
atom_spec.html#hierarchy

I hope this helps,
   Elaine
----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
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