VMD-L Mailing List

From: Shang,Emily (es3268_at_drexel.edu)
Date: Fri Aug 14 2020 - 19:14:59 CDT

Hello!

I'm looking to obtain a molecular surface. I know vmd has MSMS, quick surf, surf and sasa, but I'm looking for a molecular surface that will visualize as a surface on the molecule in the context of a larger selection.

As I understand it, a molecular surface, a vdw radius surface, and a sasa are all different, and I have had success in visualizing the latter two just not so much the first. Essentially, I'm looking for what this can do, but with a molecular surface instead, and also a surface visualization rather than points.

set all [atomselect top "chain A or chain H"]
set some [atomselect top "resid 200 to 300"]
measure sasa 1.4 $all -restrict $some -points sasapoints
foreach pt $sasapoints {
  draw point $pt

}
I aim to have the visualization look something like the automatic surface function in pymol, just on vmd.

Thank you in advance! Let me know if I should clarify, because I know a lot of previous posts on the mailing list were about sasa.
Emily