From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Aug 20 2020 - 10:58:44 CDT

Hi Emily, you can color-code the surface using any of the molecular fields
(occupancy, beta, etc) including the per-frame fields
"user" , "user1", etc

You can set occupancy and beta in a PDB file, or any of the fields from
within VMD using a script. You'll need to check the doc of atomselect and
the related get/set functions.

Giacomo

On Thu, Aug 20, 2020 at 11:53 AM Shang,Emily <es3268_at_drexel.edu> wrote:

> 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.
>
>
>
>
>

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Research collaborator, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin