VMD-L Mailing List

From: Ryan McGreevy (ryanmcgreevy_at_ks.uiuc.edu)
Date: Mon Jul 29 2019 - 14:34:30 CDT

As John mentioned, creating a mask around an atom selection is probably
what you're looking for. In the latest VMD 1.9.4 alpha builds, there is a
new tool, "voltool" for manipulating density maps. The "voltool mask"
command will mask a density around an atom selection and give you a density
of just that region. In older versions of VMD, you can create a mask using
the "volmap mask" command, then apply using "volutil -mult" command to
multiply the mask against the original density map. (The new "voltool mask"
command does the same thing, but automatically in one step so it is much
easier to use.)

On Mon, Jul 29, 2019 at 2:38 PM John Stone <johns_at_ks.uiuc.edu> wrote:

> At present, this would be best achieved by generating a so called
> "mask map" and then using it to show just the region you're interested
> in. I'm looking at modifying the way the Isosurface rep works so you
> could show map regions within a given distance to an atom selection as
> a built-in representation feature, but for the time being the mask
> map is the best way to achieve this. I'm CCing one of my colleagues
> that works on MDFF so he can give you the most efficient set of
> operations to achieve that.
>
> Best,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sat, Jul 27, 2019 at 08:02:14PM +0200, Jérôme Claverie wrote:
> > Dear users,
> >
> > I would like to observe local electron density. Is there a way in
> > VMD to look at volumetric data only in specific region, as for
> > atoms?
> >
> > Best regards
> >
> > Jérôme
> >
> >
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>
>