[Chimera-users] Coloring a surface according to distance from a selection

Elaine Meng meng at cgl.ucsf.edu
Wed Nov 21 10:03:32 PST 2007

Hi Paul,
You mentioned coloring continuously (gradual shading over a color  
range) based on distance from a point or axis, as can be done with  
Color Surface.   There is no tool that does exactly what you  
describe, coloring a molecular surface continuously based on vertex  
distance from some set of atoms, but there are some possibilities  
that may do part or all of what you had in mind:

(1) The first two ideas do not use the surface vertex coordinates.   
Instead, atoms can be selected based on their distances from another  
set of atoms, and then the surface patches that go with those atoms  
can be colored.  These also do not provide shading over a range of  
colors.  You could use successively more stringent cutoffs and get a  
series of colors that way, but they would not blend smoothly into  
each other.
   (a) select atoms in one chain within a certain distance of atoms  
in the other chain, color them, repeat with smaller cutoff if you  
want to use multiple colors
(must go larger->smaller as the opposite direction will overwrite the  
previous colors).  If you use commands rather than the menu, you can  
just specify and color in a single step without selecting.  Example  
   open 2r4s; surfcat receptor :.a; surfcat antibody :.h:.l
   surf receptor
   color pink,s receptor & antibody za<5
   color red,s receptor & antibody za<4

   (b) use Find Contacts/Clashes (or findclash command) to select  
atoms in one chain that contact atoms in the other chain, color  
them.  The advantage over (a) is that this uses different VDW radii  
for different atom types and allows compensation for hydrogen  
bonding.   Perhaps (a) is better if you want to use multiple colors,  
(b) if you want to know which atoms are really contacting.  Using the  
same example structure as in (a), for example, start "Find Clashes/ 
Contacts" (under Tools... Surface/Binding Analysis).  Select chain A  
(for example, command "sel :.a"), click "Designate" in the top  
section of the clash dialog.  In the parameters section, click  
"contact" to set suggested values for identifying contacts.  In the  
bottom section, choose only the coloring option and set the color as  
desired before clicking "Apply."  If you previously tried (a) and you  
don't see a color change in the surface when Apply is clicked, try  
using the command "~color,s" to remove those previous colors.

(2) Intersurf does continuous coloring, but as you mentioned, the  
surface is chunky and currently there is no way to increase its  
vertex density.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 21, 2007, at 4:03 AM, <Paul.Pillot at ac-nice.fr> wrote:
> Hello,
> I can color a surface according to the distance from a single point  
> or a plane, but is it possible to do it according to the distance  
> from a selection (eg an other chain or molecule) ?
> My aim is to show the contacts between an antibody and an antigen.  
> I tried the tool intersurf for doing it, but the result is pretty  
> crude (low definition of the surface compared to the usual surfaces  
> available).
> Thanks in advance,
> Paul

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