VMD-L Mailing List

From: Dudo (dudomail_at_gmail.com)
Date: Thu Aug 28 2014 - 04:55:01 CDT

you can download a 30 days trial of accelrys material studio visualizer,
and it allows you to calculate occupied, occupiable and solvent accessible
volumes
for a probe with a given radii and to visualize the surfaces. it allows you
to make a couple of things, set transparency or make a cross section.
however, an even better
implementation of this tool was in UNIX version of the software called
Cerius2, it allowed selecting particular atoms and calculating volumes only
around them.
perhaps this is possible in the scripting interface of Mat Studio. there
exists also a Linux version of this software called Insight II. but I have
no
experiences with this version. (sample
http://s30.postimg.org/y2jvd10up/free_volume.png)

D.

On Thu, Aug 28, 2014 at 10:41 AM, Norman Geist <
norman.geist_at_uni-greifswald.de> wrote:

> Hi Max,
>
> see "measure sasa", the radius of the probe can be chosen and exclusions to
> what is "space" or not can be made.
>
> Norman Geist.
>
>
> > -----Ursprüngliche Nachricht-----
> > Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im
> > Auftrag von Ebert Maximilian
> > Gesendet: Mittwoch, 27. August 2014 20:22
> > An: <vmd-l_at_ks.uiuc.edu>
> > Betreff: vmd-l: Accessible volume around an atom
> >
> > Hi there,
> >
> > I am looking for a possibility to draw in VMD a spherical volume with a
> > giving radius around an atom but only include space not occupied but
> > other molecules. For example I have a protein loaded in VMD and I draw
> > a sphere around an atom I want the sphere volume minus the protein VDW
> > volume. Is this possible?
> >
> > I am trying to display a solvent accessible volume so to speak.
> >
> > Thank you,
> >
> > Max
>
>
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