[Chimera-users] New surface coloring command

Thomas Goddard goddard at cgl.ucsf.edu
Mon Jun 22 13:45:54 PDT 2009

I added a Chimera command "scolor" that can color surfaces radially or 
according to volume data values such as electrostatic potential.  This 
command is the equivalent of the Surface Color dialog.  A few examples:

	scolor #0 geometry cylindrical

colors the surface by distance from a cylinder axis (default z-axis) 
with default coloring red-white-blue ranging from minimum to maximum 
surface radius.

	scolor #0 geom radial cmap 100,gray:150,blue:200,purple

colors radially with colors gray,blue,purple at radii of 100,150,200.

	scolor #0 volume #1 cmap -10,red:0,white:10,blue

colors surface #0 using volume data #1 with colors red,white,blue for 
volume data values -10,0,10.  Here's a summary of the full command 
syntax.  Detailed documentation will be available in the manual before 
the next Chimera release.

scolor <surfaceSpec>
    [volume <vspec>]
    [gradient <vspec>]
    [geometry radial|cylindrical|height]
    [color <color>]
    [center <x,y,z>|<atomspec>]
    [axis x|y|z|<x,y,z>|<atomspec,atomspec>]
    [coordinateSystem <modelid>]
    [cmap <v,color>:<v,color>:...|rainbow|gray|redblue|cyanmaroon]
    [cmapRange <min,max>|full]
    [reverseColors true|false]
    [colorOutsideVolume <color>]
    [autoUpdate true|false]
    [capOnly true|false]
    [perPixel true|false]


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