[Chimera-users] Virus map density versus radius
goddard at cgl.ucsf.edu
Fri Mar 2 14:59:54 PST 2007
I added a Chimera keyboard shortcut "rd" that prints out average map
density versus radius.
This zip file contains a directory RadialDensity that you put in
chimera/share. You enable keyboard shortcuts with Tools / General
Controls / Accelerators On, open your VIPER map and type shortcut "rd".
A table of radius and average density values is displayed in the Chimera
reply log. You can copy and paste it to a plotting program. I've
attached an example image for em_1sva. I used the following plotting
program on the Mac.
The calculation is very slow because it is done in Python. For
em_1sva (size 72^3) it took 12 seconds on my intel Mac and for em_1011
(size 256^3) it took 10 minutes. It could be 100 to 1000 times faster
in C++ but that would require more code. I tested with Chimera 1.2343.
I will be at the Biophysical Society meeting Sunday through Tuesday
and probably not answering email.
Padmaja Natarajan wrote:
> I was also wondering if it is possible to get "max. radius" value for
> every entry by
> radially averaging the density values for radii going in steps of the
> pixel size of that map.
> Then we do not have to give the radius value in the input text file
> and also will be able to produce a text
> file with "radius vs. average density" for each entry. Just a thought.
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