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@N :131.B@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@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@N#0.5:131@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@fourmentinguilbert.org> Pour : chimera-users@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