Simple distance to .txt scripting question
Hi everyone, I'm trying to write a script that opens a set of .pdbs, measures the distances between certain atoms, and then writes the distance to a text file for later analysis. It's easy enough to do something like...
runCommand("distance #0:519.A@NZ #:1.Y@O4")
...which executes the command and appends the info to the reply log ("Distance between #0 LYS 519.A NZ and #5 X01 1.Y O4: 2.33"). What I'd like to do is have that actual measured distance (2.33) be stored in a variable that I could then write to a text file (I know how to do this bit). Thanks for any thoughts! --Andrew -- Andrew Hagen PhD candidate - Plant and Microbial Biology UC Berkeley - Keasling group
Hi Andrew, So, first select the two atoms somehow (e.g. "sel #0:519.A@NZ #:1.Y@O4"), then do this to get the distance into a variable 'd': import chimera atoms = chimera.selection.currentAtoms() d = atoms[0].xformCoord().distance(atoms[1].xformCoord()) --Eric Eric Pettersen UCSF Computer Graphics Lab On Dec 9, 2011, at 5:35 PM, Andrew Hagen wrote:
Hi everyone,
I'm trying to write a script that opens a set of .pdbs, measures the distances between certain atoms, and then writes the distance to a text file for later analysis. It's easy enough to do something like...
runCommand("distance #0:519.A@NZ #:1.Y@O4")
...which executes the command and appends the info to the reply log ("Distance between #0 LYS 519.A NZ and #5 X01 1.Y O4: 2.33"). What I'd like to do is have that actual measured distance (2.33) be stored in a variable that I could then write to a text file (I know how to do this bit).
Thanks for any thoughts!
--Andrew
-- Andrew Hagen PhD candidate - Plant and Microbial Biology UC Berkeley - Keasling group
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participants (2)
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Andrew Hagen -
Eric Pettersen