Andrea,

I've made a script that does approximately what is in your picture. You give it two atom selections, and it will display the VDW radii of atoms in one group that intersect with the other group. A red line (it's really a bunch of small red spheres, but I think it looks fine) is added at the intersection.

Opening the script will add the "displayClash" command. To make the attached image, I defined a selector called "BINAP" and another called "EDA" for the two ligands on this structure. Then, I ran "displayClash EDA with BINAP". The command also has a 'scale' option to scale the VDW radii, and a 'color' option to change the intersection color (e.g. "displayClash EDA with BINAP scale 1.2 color purple").

If you don't want to see the red intersection through the VDW radii, you can make it slightly transparent. ChimeraX doesn't display transparent things that are behind other transparent things.

I've attached the Python script as a .txt file because Outlook doesn't like Python files. You'll have to change the extension to .py before trying to open it in ChimeraX.

Best,

Tony

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From: ChimeraX-users <chimerax-users-bounces@cgl.ucsf.edu> on behalf of Andrea Dallapè via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: Saturday, May 21, 2022 4:38 PM
To: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] (no subject)

 

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]

Dear ChimeraX Team,

I would like to ask you if there's a simple and easy method (without using external software) to label the steric clashes, as in the attached image (the red line between the ball densities).

Thank you for your help and attention!

Andrea