[Chimera-users] selecting

Ann Mullin amullin at tulane.edu
Tue Jan 18 09:07:00 PST 2005

As another fairly newbie, may I also suggest using the sequence window,  
setting the selection mode on 'Append', and using the mouse to select  
the residues you want. For me this is easier than the typing.

Ann Mullin
Research Scientist
Cell and Molecular Biology Dept.
Tulane University
New Orleans, LA 70118-5698
504-865-6742 (Ph)
504-865-6785 (FAX)
amullin at tulane.edu
On Jan 17, 2005, at 12:21 PM, Elaine Meng wrote:

> 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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> Chimera-users at cgl.ucsf.edu
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