[Chimera-users] Adding quadrant lines to atoms

[Eric Pettersen]

Hi Trevor,
	There isn’t a direct way to do it, but Chimera’s Thermal Ellipsoids tool (in the Structure Analysis category) has this depiction for structures with anisotropic B-factor information (ANISOU records in PDB files).  If your structure doesn’t have such information, you can add fake information to the structure and fool Thermal Ellipsoids into rendering the depiction.  The following Python code will add fake anisotropic B-factor information to the structures atoms:

import numpy
import chimera
for a in chimera.openModels.list()[0].atoms:
	a.anisoU = numpy.identity(3, dtype=numpy.float32) * a.radius

I have attached a file with the above Python in it.  Just open the file after you open your structure.  Then with the Thermal Ellipsoids tool you should be able to get something like this:



You would use the “Octant lines” preset of the tool.  I also changed the scale factor in the tool to 0.25.  To get the black bonds, select the whole structure (Select->Select All) and then bring up the Selection Inspector (magnifying-glass icon at the bottom right of the Chimera window).  Change the Inspect category to “Bond”, and then “halfbond mode” to “off”, “radius” to 0.1, and “color” to black.  You can change the background to white either with the command “set bgcolor white” or Actions->Color->all actions… and in the resulting dialog change “…applies to” to “background” and click on white.

—Eric


	Eric Pettersen
	UCSF Computer Graphics Lab




> On Apr 19, 2018, at 2:26 PM, Trevor Harris <trevorha at sas.upenn.edu> wrote:
> 
> Hi, 
> 
> Is there a way to add quadrant lines to atoms similar to how Houkview does it in CylView, pictured below. If not, could you add this feature as an option?
> <PastedGraphic-3.tiff>
> All the best,
> Trevor Harris
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