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
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
participants (2)
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Damien Larivière -
Elaine Meng