[Chimera-users] Radial color solid style map display
goddard at sonic.net
Mon Jul 23 11:55:27 PDT 2012
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 Veesler
> Research Associate
> The structural Virology lab - Johnson's lab
> Department of Molecular Biology
> The Scripps Research Institute
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