VMD-L Mailing List

From: Jordi Cohen (jordi_at_ks.uiuc.edu)
Date: Wed Jun 20 2007 - 21:56:08 CDT

Lutz,

There might indeed be an error in the volmap docs, I'll go fix it.

To get a minmax, volmap takes your selection's size and pads it by a
certain amount that is selection- and maptype-dependent (e.g., 3-
sigmas for density maps). This is absolutely necessary to always get
properly-looking maps.

To accomplish what you want, you may wish to try something like this
(i don't have VMD in front of me, so I'm hoping it will work as-is):

   set sel [atomselect top all]
   volmap density $sel -minmax [measure minmax $sel]

or something of that order...

Cheers,
Jordi

On Jun 20, 2007, at 8:35 PM, Lutz Maibaum wrote:

> Hello,
>
> I was wondering if the documentation of the "volmap" command [1]
> contained
> an error. I believe that instead of
> volmap <atom selection> <maptype>
> it should be
> volmap <maptype> <atom selection>
>
> Also, what is the default range for which the volumetric map is
> computed if
> the -minmax option is not specified? I run into problems with the
> default
> setting for my trajectories, where VMD has the correct unit cell
> information (as shown by "pbc get"), but the volume used for the
> gridding
> is larger than that:
>
> vmd > pbc get
> {86.177399 86.177399 86.177399 90.000000 90.000000 90.000000}
> vmd > volmap density [atomselect top "all"] -res 1.0
> volmap: Computing bounding box coordinates
> volmap: grid minmax = {-11.000000 -11.000000 -11.000000} {97.000000
> 97.000000 97.000000}
> volmap: grid size = 109x109x109 (4.9 MB)
>
> I can use the -minmax option to restrict the range to the actual
> box size,
> but I was wondering if there was a way to do this automatically.
>
> Thanks,
>
> Lutz
>
>
> [1] http://www.ks.uiuc.edu/Research/vmd/current/ug/node141.html#7633