[Chimera-users] Fwd: distance between 2 residues

[Elaine Meng]

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:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/quickref.pdf>

...and more details in the "atom spec" manual page:
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html 
 >

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  
command:

distance sel

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



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