[Chimera-users] question

Elaine Meng meng at cgl.ucsf.edu
Thu Feb 23 15:20:08 PST 2006

Hi Stefano,
In the future, we plan to make it possible to select only particular  
chains in particular models with the Select menu.  For now, however,  
there are several ways to select chains specifically or to select  
whole models (each PDB file is treated as a "model"):

(1) By picking from the graphics window.  Ctrl-click on an atom or  
bond in the chain or model of interest to select the atom or bond.   
Hit the up arrow key once to promote the selection to the whole  
residue, again to promote it to the whole chain, again to promote it  
to the whole model. You can hit down arrow if you accidentally  

(2) With the select command. Say you have model 0 with chains A,B,C,D  
and model 1 with chains A,B. To select just model 1, use the command:
select #1

To select just chain A in model 1, use the command:
select #1:.a

To select just residues 10-20 and 25 in chain A in model 1, use the  
select #1:10-20.a,25.a

(3) With the Model Panel. Open the Model Panel (Tools... General  
Controls... Model Panel). To select one or more whole models, choose  
them in the left side of the Model Panel, then click "select" on the  
right.  You can choose more than one model at once using Ctrl-click  
or Shift-click. To select only particular chains from those models,  
go to the "infrequently used" functions in the Model Panel, then  
click "select chain(s)" - that will bring up a panel in which you can  
check a box next to each chain you want to select. (with the  
Configure button, you can control which functions are considered  
"frequently used" or "infrequently used")

I hope this helps!

  On Feb 23, 2006, at 2:39 PM, Stefano Ciurli wrote:

> Hello, I am a new user of Chimera and I need to ask a question: let's
> say that I am loading several PDB files from the RCSB, all of them
> belonging to the same protein, the latter having 3 subunits A, B, and
> C. I need a way to operate on single PDB files (select and manipulate
> features of each PDB file at once). How do I do it? I can easily find
> the select->chain option, but it would operate on all chains of that
> type in all PDB files.
> Regards,
> Stefano

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

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