[Chimera-users] Virus map density versus radius

[Tom Goddard]

Hi Padma,

  I added a Chimera keyboard shortcut "rd" that prints out average map 
density versus radius.

    
https://www.cgl.ucsf.edu/cgi-bin/chimera-get.py?file=experimental/radialdensity.zip

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.

    http://www.apple.com/downloads/macosx/math_science/plot.html

  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.

    Tom

Padmaja Natarajan wrote:
> Tom,
>
> 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.
>
> Thanks
> Padma
>

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