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

Tom Goddard goddard at cgl.ucsf.edu
Wed Nov 21 10:08:57 PST 2007

Hi Paul,

  The usual approach for coloring a molecular surface is to color the 
nearby atoms.  The surface is by default colored to match colors of the 
closest atoms.  First you select the atoms near the antigen - antibody 
interface.  I'm not sure what the obvious and simple way is to do that 
task.  But you can select the antigen, then use Tools / Higher Order 
Structure / Multiscale and press the "Contacts" button.  Then color 
those atoms with the Actions / Color menu.  Clear the selection (ctrl 
click on background) then use Actions / Surface / Show to get the high 
resolution molecular surfaces.

  Sounds like you have tried the Surface Color tool.  That won't color 
by distance from a selection (though maybe it should).  That operation 
is done by the Color Zone tool (Tools / Volume Data menu) but that only 
works on volume contour surfaces, not molecular surfaces.  That quirky 
limitation will be removed in the next release but that is 6 months away.


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