VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 01 2012 - 14:19:18 CST
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Ben,
Which exact parameters did you use when you ran the volmap calculation?
The defaults I'd expect in the VolMap GUI are (for "occupancy"):
Resolution: 1.0A
Compute for all frames, combine using: Average
I assume you didn't check the "use point particles (radius = 0)" box?
Cheers,
John Stone
vmd_at_ks.uiuc.edu
On Tue, Jan 31, 2012 at 01:32:50PM +0000, Benjamin Hall wrote:
> I thought that, but the regions of highest occupancy are picked out with an isovalue of 1.5. If this is just the average number of atoms it would make sense but I can't find it documented anywhere and wanted to be sure
>
> Best wishes
>
> Ben
>
> --
> Dr Benjamin A Hall
> Centre for Computational Science, Department of Chemistry, UCL
> benjamin.a.hall_at_ucl.ac.uk
>
> On 31 Jan 2012, at 13:25, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> > On Tue, Jan 31, 2012 at 7:01 AM, Ben Hall <benjamin.a.hall_at_ucl.ac.uk> wrote:
> >> I've been using the volmap tool to pick out areas of high water occupancy
> >> in MD simulations, and wondered if it was possible to link the specific
> >> value of an isosurface to a calculated density (ie 1 = 50 % occupancy)?
> >
> > well, shouldn't a value of 0.5 be equivalent to 50% occupancy?
> > provided you don't use any other scaling, that is.
> >
> > axel
> >
> >>
> >> Thanks in advance
> >>
> >> Ben Hall
> >>
> >> --
> >> Dr Benjamin A Hall
> >> Centre for Computational Science, Department of Chemistry, UCL
> >> benjamin.a.hall_at_ucl.ac.uk
> >>
> >>
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
-- NIH Resource 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/ Fax: 217-244-6078
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