[Chimera-users] Radial color solid style map display

Tom Goddard goddard at sonic.net
Mon Jul 23 11:55:27 PDT 2012

Hi David,

   Radially coloring using solid style map display doesn't work. Solid 
style display of a single plane with volume viewer uses a gray-level 
coloring of the plane.  The Surface Color tool and other coloring tools 
in Chimera replace the coloring of a surface and aren't able to modulate 
the existing (gray-level) coloring.

   But there are often tricky ways to get what you want.  I've attached 
a picture of a radial color of a plane of an HIV tomogram.  I did it by 
opening the map twice.  With the first copy I display the solid style 
plane.  With the second copy I display one plane in surface style with a 
low contour level.  Then I placed a marker (volume tracer) at the center 
of a virus on that surface and used surface color to color that surface 
radially (scolor command).  Then I made that surface transparent 
(command "transp 90 #1" in Chimera daily build).  It didn't look good 
because the two planes were coincident which created artifacts, so I 
froze the first map (Model Panel, deactivate) and moved the second one a 
tiny bit in front.  Also I made the background color gray -- black or 
white give somewhat different appearance.

     You could also layer a transparent radial colored layer on top in 
PhotoShop or Gimp I bet.


> Hi Tom,
> I'm writing as I would like to color by radius an EM map but when it is displayed as a single plane of width=1 pixel.
> Is this possible?
> Thanks a lot
> David
>    David Veesler
> Research Associate
> The structural Virology lab - Johnson's lab
> Department of Molecular Biology
> The Scripps Research Institute

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