From: Vermaas, Josh (
Date: Fri May 06 2022 - 15:44:01 CDT

Sure. Atomselections can use geometry to define them. So if you wanted to select everything *except* a cylinder, you have something like this be your atomselection text: “not (x*x+y*y < 25)”. See also


From: <> on behalf of Mohammed GOUNZARI <>
Date: Friday, May 6, 2022 at 4:32 PM
To: "" <>
Subject: vmd-l: remove atoms in a geometric shape using VMD

Hello All,
I am trying to remove atoms from a sample to create circular holes in it and I do not know if it is possible using VMD. And if it is possible can you please share the way to do it. thank you in advance


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