[Chimera-users] selection of some chain but not some particular residue

[Elaine Meng]

>
> On Sep 5, 2007, at 3:30 PM, Dhiraj Srivastava wrote:
>        I am new to Chimera and i have hard time finding commands  
> like how to select some chain and exclude 1 or 2 residue in that  
> chain?

Hi Dhiraj,
There is an "atom specification" syntax that allows you to say  
exactly which chains, residue numbers, atoms you want.  In brief, #  
means model, : means residue, @ means atom name.  There are many  
examples throughout the documentation, so I'll give one example in  
this mail and some links to more information:

disp :25-30.a,30.b,10
   - display residues 25-30 in chain A, residue 30 in chain B, and  
residue 10 in all chains

Here is the "atom specification" man page, includes some examples:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/ 
frameatom_spec.html
(besides just using chain, residue, atom name, you can do all kinds  
of fancy things such as in helix only, near a ligand, etc.)

This PDF help sheet has a bunch of examples on its second page:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf

>  also i have a protein with 2 chain. how can i make different model  
> for different chain or different portion of same chain so i can  
> perform some action like clipping on these model independentaly?  
> can any one please help me for these problems?

You can open the same structure more than once, and then delete  
different parts from the different models.  For example, if the  
structure has chain A and B, open it twice to put it in models 0 and  
1, then use these commands:
command:  delete #0:.b
command:  delete #1:.a

Then model 0 will just have chain A, model 1 will just have chain B.   
You could instead undisplay (~display) instead of using delete, but I  
think deleting is easier - later you can't get confused and  
accidentally display those other parts.   Another way is to use a  
text editor and make new PDB files with just the parts you want  
before opening them in Chimera, but that is probably less convenient.

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco
                      http://www.cgl.ucsf.edu/home/meng/index.html