[Chimera-users] radial density map

Tom Goddard goddard at sonic.net
Mon Feb 9 13:17:51 PST 2015

Hi Jian,

  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


There is an old mailing list message I wrote about that extension

	http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008697.html <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2013-April/008697.html>

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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