VMD-L Mailing List

From: Shang,Emily (es3268_at_drexel.edu)
Date: Thu Aug 20 2020 - 10:12:18 CDT

Hi Norman,

Unfortunately, while those commands give me the residues I want, I'm looking for a way to visualize their surface area in context to a larger surface area. Quick surf and msms seem to only give the surface area of the residues by themselves.

Thank you,
Emily
________________________________
From: Norman Geist <norman.geist_at_uni-greifswald.de>
Sent: Thursday, August 20, 2020 3:24 AM
To: Shang,Emily <es3268_at_drexel.edu>
Cc: vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: AW: vmd-l: How do I define "collision only" atoms using MSMS?

External.

Hey,

what about:

atomselect macro protein1 {any selection for protein1}

atomselect macro protein2 {any selection for protein2}

Now in drawing methods choose MSMS (or better Quicksurf imho) and as selection use something like:

same residue as ((protein1 within 2.5 of protein2) or (protein2 within 2.5 of protein1))

You could also split them in two representations, depending on what looks better:

same residue as (protein1 within 2.5 of protein2)

same residue as (protein2 within 2.5 of protein1)

Also, if you want to play over multiple frames, consider checking the “Update selection every frame” box on the Trajectory tab in the representations.

Bests

Norman Geist

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von Shang,Emily
Gesendet: Mittwoch, 19. August 2020 17:24
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: How do I define "collision only" atoms using MSMS?

I'm trying to illustrate only the buried surface between two proteins.