[Chimera-users] Radial density plots

Tom Goddard goddard at sonic.net
Mon Apr 15 10:14:56 PDT 2013


Hi Pranav,

  The Chimera radial map density code I gave to Padma (in 2007) was a 
simple Chimera extension in a directory called RadialDensity. You either 
put the RadialDensity directory in the chimera/share directory (on Mac 
Chimera.app/Contents/Resources/share) or you can put it somewhere else 
for example /Users/me/chimera-stuff/RadialDensity then add the parent 
directory (e.g. chimera-stuff) using Favorites / Preferences, category 
Tools, Add....  After doing either of these install steps Chimera will 
have a keyboard shortcut "rd" that prints the density values as a 
function of radius (in steps equal to the map grid spacing).  You can 
plot those with whatever plotting application you want.  To run the 
shortcut you can use the command "ac rd", or enable keyboard shortcuts 
(using Tools / General Controls / Keyboard Shortcuts) and just type rd.

   I've put the RadialDensity extension on the Chimera Python scripts 
web page.

     http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts

I've attached a plot I made with it of a bacteriophage (EMDB 1011).

     Tom



-------- Original Message --------
Subject: [Chimera-users] Radial density plots
From: Pranav Shah
To: chimera-users at cgl.ucsf.edu
Date: 4/13/13 8:04 PM
> Hi Tom,
>
> I am trying to plot a graph of  average density as a function of radius in Chimera v1.7.  I tried the code that you wrote for Padma in an earlier post. However, Chimera spits up this error
> "Accelerators file C:\Program Files\Chimera 1.7\share\Accelerators\radial_density.py has no register_accelerators() function." when I try to load the radial_density.py in the keyboard shortcuts menu.
> Could you tell me how this bug can be fixed?
>
> Awaiting your assistance,
>
> Warm regards,
>
> Pranav Shah
> Postgraduate student (Infection and Immunobiology),
> College of Medical, Veterinary and Life Sciences,
> Institute of Infection, Immunity and Inflammation,
> University of Glasgow,
> Glasgow, Scotland,
> UK.
> _______________________________________________
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>

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