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 http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts 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. Tom
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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>