VMD-L Mailing List

From: Keith Refson (kr_at_isise.rl.ac.uk)
Date: Sat Nov 22 2003 - 11:16:30 CST

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