Chimera does not make radial density plots. I guess you found the RadialDensity.zip extension which creates the “rd” shortcut on the Chimera scripts web page

which says that it prints to the Chimera reply log the average radial density as a function of distance from the center. Make sure your map origin is at the center of the virus (volume dialog menu Features / Coordinates, Origin Index value). You can plot that data in any graphing program. Each value is the average over a thin spherical shell so it does not depend on any axis. This won’t help you if you just want the density on a 1-dimensional line coincident with a symmetry axis.

On Feb 9, 2015, at 9:55 AM, Jian Guan wrote:

Hi all,
I have a mrc map of virus, T=7 icosahedron. Does anyone know how to make radial density map (averaged radial density VS radius of virion)?
I tried chimera method of shortcut rd. It took long time but return one result. For the rd result, is it make along x, y or z axis? Or along assigned axis, like 5 fold symmetric axis? I have asymmetric extra density around 5-fold axis. What will happen in my case if use rd?
Are there any other ways to make the plot besides of rd?
Thank you so much.
Sincerely yours,
Jian
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