VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Dec 01 2003 - 17:27:09 CST

Keith,
  At present we don't have a way to color the isosurface representation,
but the long-term plan is to have 3-D texturing appicable on any
representation from volumetric data. What sort of coloring were you
hoping to put on an isosurface? Since the isosurface itself represents
the surface corresponding to a single value, it wouldn't be colored by the
density map it came from, but I could see applying colors from a
_different_ data set. Is that what you had in mind? Also, in the
current (and soon to be released 1.8.2 version) there's no way to alter
or warp the density map axes, but this could probably be added in the
next major rev of VMD without much difficulty. Until then, you'd have to
do it in your own Tcl script, loading the data yourself with the 'mol volume'
command, in which you'd be able to specify the axes for the data set yourself,
which I realize is inconvenient, but this is something we'll be working on
for the next major rev of VMD...

You can display the unit cell for the volumetric data using the
"box only" mode in the isosurface rep. Its the same for both the volume
slice and isosurface reps. Perhaps this would be best factored out as a
separate representation or a checkbox of some sort, but for now that's
where it stands.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Nov 22, 2003 at 05:16:30PM +0000, Keith Refson wrote:
> I'm attempting to display an electron density map superimposed on a
> crystal structure. The structure is in a rhomohedral (highly
> non-orthogonal) unit cell. This makes rendering an volumetric slice
> problematic as the slice plane lies orthogonal to the *cartesian*
> axes, which make an irrational angle with the crystallographic unique
> axis.
>
> It is easy enough to re-orient the crystal structure so the
> rhombohedral axis lies along Z by specifying the SCALE1 records in the
> PDB file appropriately. But I also need to re-orient the electron
> density map in space.
>
> Can anyone suggest how to re-orient the electron density map by a
> given matrix?
>
> While posting, I might as well ask two further questions.
>
> 1) Is it possible to colour the isosurface representation?
>
> 2) Is there any way of displaying the unit cell axes in the volumetric
> slice plane representation?
>
> Thanks for any help
>
> sincerely
>
> Keith Refson
> --
> Dr Keith Refson,
> Building R3
> Rutherford Appleton Laboratory
> Chilton
> Didcot
> Oxfordshire OX11 0QX
> T: 01235 446652 K.Refson@
> F: 01235 445720 @rl.ac.uk 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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