[Chimera-users] Fwd: distance between 2 residues

Elaine Meng meng at cgl.ucsf.edu
Mon Jan 17 12:41:20 PST 2011

Hi Damien,
It is not necessary to use model numbers.  You can just open the  
original file and then give the chain IDs in the atom specification,  
for example, in the command:

distance :246.A at N :131.B at N

measures between N in residue 246 in chain A and N in residue 131 in  
chain B.  There are examples of command-line specification in the  
Chimera Quick Ref (PDF), see the second page:

...and more details in the "atom spec" manual page:

Or, if you can find the atoms in the display window, Ctrl-click to  
select one, Shift-Ctrl-click to select the second, and then use the  

distance sel

I hope this helps,
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

On Jan 17, 2011, at 10:12 AM, Damien Larivière wrote:

> Hi everyone,
> As explain in the Chimera user guide, I used the command such like  
> distance  #0.2:246 at N#0.5:131 at N to measure the distance between two  
> atoms of interest.
> To be more explicit regarding my first email, it was necessary to re- 
> edit the pdb file and to assign a model number to each chain. In the  
> example above, the chain B is named model 2 (then model 0.2 in  
> Chimera) and the chain D is named model 5 (then model 0.5 in Chimera).
> It works fine but I suppose that there is a simpler and more direct  
> way to specify the chain in the command?
> Many thanks
> Damien
> -------- Message original --------
> Sujet:
> distance between 2 residues
> Date :
> Mon, 17 Jan 2011 18:09:11 +0100
> De :
> Damien Larivière <damien.lariviere at fourmentinguilbert.org>
> Pour :
> chimera-users at cgl.ucsf.edu
> Dear all,
> I would like to know the (mean or approximative) distance between two
> residues within a protein (let's say Res 5 of chain A and Res 246 of
> chain C).
> I suppose that I have to select one atom in each of the residues and  
> use
> the Distance tool. I confess I have trouble to do so, either by  
> picking
> in the viewport or by using the atom identifier. May you tell me a
> simple way to achieve such a distance?
> Many thanks for your help
> Damien

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