VMD-L Mailing List

From: Vermaas, Josh (vermaasj_at_msu.edu)
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 https://www.ks.uiuc.edu/Research/vmd/current/ug/node95.html

-Josh

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Mohammed GOUNZARI <gounzari.mohammed_at_gmail.com>
Date: Friday, May 6, 2022 at 4:32 PM
To: "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
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
cordially

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"Nothing can stop a good scientist."
Dr. E. L. Brown, Back to the Future III

GOUNZARI Mohammed
Mail: gounzari.mohammed_at_gmail.com<mailto:gounzari.mohammed_at_gmail.com>
Phone: +212699554615