VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue May 29 2007 - 10:07:15 CDT

Hi,
  In order to display multiple probability density isosurfaces, you can
select different isovalues, coloring each one by manually selected color IDs,
or using the "color by volume" option, and having VMD automatically apply
a color scale to the data. The advantage to using the color by volume approach
is that you can then copy that representation a few times adjusting the
isovalues as appropriate, and you'll be able to see multiple individually
colored density shells quite readily. Another technique that is often handy
for this type of visualization is to use clipping planes to slice open the
isosurfaces so you can clearly see the nested shells of probability density.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, May 29, 2007 at 01:43:46PM +0100, Kailee wrote:
> Dear all,
>
> Thank you for your reply, can I ask how to view the results of volmap? Here
> is how I generated the map:
> In the selection, I typed "resname O2"; and the molecule used is "top";
> volmap type chosen is "occupancy", "avg" for all frames, the output file was
> written to "volmap_out.dx" file, after create map, I got the volmap_out.dx
> file and also a checkpoint file which is empty.
>
> Then I tried to view the map file, so I loaded volmap_out.dx into the same
> molecule, and I changed drawing method to 'isosurface', but nothing appeared
> in the screen, and as I changed isovalue, there are something started to
> appear, can I ask how to decide how big should the isovalue be?
>
> Also, as the using the volmap, the occupancy is averaged during all frames,
> is there anyway to display using different colors for
> different occupancy densities during a trajectory? so that I can see at what
> region did the gas visited most?
>
> Thank you for any suggestions in advance!
>
> Best regards,
> kailee
>
>
>
> On 5/28/07, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >
> >Hi,
> >Yes, the volmap command can do this for you. The occupancy
> >volmep essentially averages the occupancy of each of the voxels
> >in the map over a trajectory, for the given selection. If a
> >voxel is occupied, then for that frame, it gets a "1", if not,
> >it gets a "0", and the occupancy is summed over all frames
> >and renormalized at the end.
> >
> >Cheers,
> >John Stone
> >vmd_at_ks.uiuc.edu
> >
> >On Sun, May 27, 2007 at 06:54:12PM +0100, Kailee wrote:
> >> Dear all,
> >>
> >> I have a trejectory file from AMBER md calculation (.mdcrd file) on gas
> >> molecules diffusion into a protein, what I want to do now is to draw a
> >> density map of trajectories for all gas molecules across all the frames,
> >can
> >> I ask is this what occupancy volmap does or is there any script can do
> >this?
> >> Thank you for any help in advance!
> >>
> >> Best regards,
> >> Kailee
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> >WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> > 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078