[Chimera-users] zone tool in volume rendering

Thomas Goddard goddard at cgl.ucsf.edu
Thu Feb 14 14:32:48 PST 2008

Hi Jeff,

   The capability you need is to make a mask (integer array) that 
records which region each grid point belongs to.  Then you would be able 
to choose colors for each numbered region.  You could define the regions 
using the "mask" command which can currently only make a new map.  This 
support for masks does not exist yet in Chimera.  I intend to add 
support for masks this year.

   So the current ways of coloring surfaces are: color zone dialog 
(color points near markers), surface color dialog (color according to 
values in a second map, or gradients of a map, or by radius, or height 
above a plane), or single color.  Those methods are for surface/mesh 
coloring.  For solid style volume rendering it is only possible to color 
according to the grid point values.  These coloring methods are limited 
by the user interface.  The underlying rendering code can color a 
surface or solid in any way you like, though defining other colorings 
requires writing Python code.


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