VMD-L Mailing List

From: Smith, Harper E. (smith.12510_at_buckeyemail.osu.edu)
Date: Fri Oct 27 2023 - 15:40:40 CDT

You could write an xyz format file<https://www.ks.uiuc.edu/Research/vmd/plugins/molfile/xyzplugin.html> with your coordinates, then I think you could load the coordinates with mol<https://www.ks.uiuc.edu/Research/vmd/current/ug/node140.html> new.

If you just want to display spheres, you can use VMD graphics<https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.1/ug/node128.html> primitives. You can draw spheres and set their color/radii individually. 'graphics delete all' will clear everything.

Best,
Harper
________________________________
From: owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of Kevin Lin <klin665_at_uchicago.edu>
Sent: Friday, October 27, 2023 4:16 PM
To: VMD Mailing List <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: Creating Dummy Atoms in VMD Using TCL Script

Hello, I'm attempting to create some dummy atoms in VMD through the use of a TCL script. My TCL script can currently generate the locations of these atoms (x, y, z) coordinates, as well as an additional value that I could store in the beta

Hello,

I'm attempting to create some dummy atoms in VMD through the use of a TCL script.

My TCL script can currently generate the locations of these atoms (x, y, z) coordinates, as well as an additional value that I could store in the beta value for the atom. I'm struggling however to find how to actually tell VMD to display and store these atoms.

What is the best way to go about this process? I don't want to create a new molecule for every new atom as I have around 4000+ to model, so is there an easy way to generate a pdb of such atoms for VMD to consider as a single molecule? Additionally, how would I get VMD to display these atoms per say, spheres with a radius of 1A?

Any pointers would be helpful.

Thanks!