[Chimera-users] Radial density plots
goddard at sonic.net
Mon Apr 15 10:14:56 PDT 2013
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
I've attached a plot I made with it of a bacteriophage (EMDB 1011).
-------- 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,
> Chimera-users mailing list
> Chimera-users at cgl.ucsf.edu
-------------- next part --------------
A non-text attachment was scrubbed...
Size: 31439 bytes
Desc: not available
More information about the Chimera-users