VMD-L Mailing List

From: bharat gupta (bharat.85.monu_at_gmail.com)
Date: Mon Nov 04 2013 - 07:47:29 CST

Sir,

Sorry for not framing my question properly. What I want is a final number
for density around those residues. For eg, in this thread some one has
pointed out the values that were obtained after doing volmap calculations :
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/14404.html

On Mon, Nov 4, 2013 at 10:31 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Mon, Nov 4, 2013 at 1:41 PM, bharat gupta <bharat.85.monu_at_gmail.com>
> wrote:
> >
> >
> >
> > Thanks for the reply Sir,
> >
> > I got the volmap.dx file and I visualized it also, using Isosurface
> > representation. But I want to know that final average value . I checked
> the
> > volmap.dx file there are three columns with lots of zeros and sometimes
> some
> > values ... But still I didn't find the way to get the averaged value ??
>
> i don't understand the question. these numbers *are* the averaged
> values. one for every grid point.
>
> axel.
>
>
> >
> >
> > On Mon, Nov 4, 2013 at 9:24 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
> >>
> >> On Mon, Nov 4, 2013 at 11:49 AM, bharat gupta <bharat.85.monu_at_gmail.com
> >
> >> wrote:
> >> > Hi,
> >> >
> >> > I have used the volmap plugin to calculate the water density around
> >> > residues
> >> > 115-118 of my protein. I checked it by displaying it as an
> isosurface. I
> >> > want to know whether is it possible to get the final average value
> >> > (i.e.
> >> > water density averaged over all time steps) used to depict the plot??
> >>
> >> yes, if you check the "compute for all frames" button.
> >>
> >> http://www.ks.uiuc.edu/Research/vmd/plugins/volmapgui/
> >>
> >> you can have the final data either added to your molecule or saved as
> >> a .dx file.
> >>
> >> axel.
> >>
> >> >
> >> >
> >> > Thanks in advance for help..
> >> >
> >> > Regards
> >> > -----
> >> > Bharat
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> >> International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
> >
> >
> >
> >
>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy.
>