[Chimera-users] Writing data to a text file

Elaine Meng meng at cgl.ucsf.edu
Mon Nov 8 08:05:18 PST 2021

Hi Prathvi,
You can get all-by-all distances written to a file or the Reply Log by using Find Clashes/Contacts or the clashes command, by defining residue-A as the first set of atoms, residue-B as the second set of atoms, and and using a large negative cutoff value that will just get everything.  For example, if it's residue 10 in chain A of model 0 versus residue 50 in chain B of model 1, the command to send info to the Log could be something like

findclash #0:10.A  test #1:50.B overlap -1000 log true

(and/or use the saveFile option to save to file)

Find Clashes/Contacts tool

findclash command and its options

ChimeraX (our newer program) also has a tool and command to do this same thing, if you're interested.

I hope this helps,
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Nov 8, 2021, at 3:39 AM, Prathvi Singh via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hi,
> Suppose I want to find the distance between all atoms of residue-A and residue-B & write the distances to a file. Is it possible to do so in a meaningful way?

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