From: Tom Goddard <goddard@sonic.net>
Sent: Tuesday, September 28, 2021 8:54:48 PM
To: Vorländer,Matthias Kopano <matthias.vorlaender@imp.ac.at>
Cc: chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edu>
Subject: Re: [chimerax-users] Possible to measure the shortest distance between two models?

You can use Python in ChimeraX to find the shortest distance. Here is some example code closest.py to do that.

https://rbvi.github.io/chimerax-recipes/closest/closest.html

If you open that Python code in ChimeraX it registers a command "closest"

open 7LUP

closest /A to /B maxDist 100

> Minimum distance 2.27 between /A LYS 45 NZ and /B ASP 522 OD1

Tom

On Sep 28, 2021, at 2:15 AM, Vorländer,Matthias Kopano via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear all,

I am interested in measuring the shortest distance between two models (PDBs) without a priori knowledge of which atoms will be the closest ones. I am planning to do this for a large number of model pairs, therefore it would be great if this would be scriptable. Is this possible using ChimeraX?

Thanks a lot in advance,

Best,

Matthias

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