Hi Brandon,
What you want is not possible. But, if you make a pdb file
containing the atoms involved in flexible bonding and a
pdb with the atoms involved in rigid bonding, you can get
the image you want.
load Protein, protein.pdb
load Flex, flexible.pdb
load Rigid, rigid.pdb
hide everything
show sticks, Flex
show sticks, Rigid
show spheres, Protein
set sphere_scale, 0.3
set stick_radius, 0.15
color red, Flex
color blue, Rigid
That should basically get you close to what you want.
Hope ti helps,
Tsjerk
On Wed, 25 May 2005 17:21:23 -0700
Brandon Hespenheide <brandon.hespenhe...@asu.edu> wrote:
Hi,
In general, coloring of a molecule is mapped
onto the atoms.
For example carbon = green, hydrogen = gray. The bond
between the carbon
and the hydrogen would then be two-tone; half of the
bond nearest the
carbon would be green, the other half of the bond
nearest the hydrogen
would be gray.
Is it possible to color the bonds in a
molecule independent
of the atoms they are incident with? We have some
software that computes
which bonds in a molecular structure can rotate
(flexible) and which can
not rotate (rigid). I'd like to be able to distinguish
these bonds
(flexible versus rigid) with different colors.
The problem is that atoms can be incident with both
flexible bonds and
rigid bonds, so we can't simply color an atom
appropriately.
Something like "atom_1 atom_2 color" would be
nice.
Any thoughts?
Brandon Hespenheide
