[Chimera-users] Defining planes & Thermal ellipsoids

Elaine Meng meng at cgl.ucsf.edu
Sat Feb 20 10:26:16 PST 2010

Hi Dave,
If you just want to fill rings, use the "fillring" command:

or you can create arbitrary polygons with BILD format:

The reason to use planes from Axes/Planes/Centroids is that they are  
"smart" objects that can be used in distance and angle measurements  
with atoms, axes, and centroids, as alluded to in my other replies  
today.  If display is all you are concerned with, either of these  
other methods will suffice.

In Thermal Ellipsoids, the probability is working fine for me.  You  
enter a number in the probability area and press return, which will  
accordingly adjust the number shown in the "Scale factor" field.  Then  
that scale factor will be used the next time you click "Show  
Ellipsoids" or choose one of the Thermal Ellipsoid presets.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Feb 20, 2010, at 7:07 AM, David Chenoweth wrote:

> Hi!
> Thanks so much for adding the define plane and define centroid  
> features. Is there any way to add the option of defining the border  
> of the plane as a polygon where the selected atoms define the  
> polygon vertices? This would allow a plane in the shape of a hexagon  
> or any other heterocycle to be inset inside of an aromatic ring for  
> example without the edges of the plane being visible outside the  
> bond enclosed area.  Also, the thermal ellipsoid feature looks  
> fantastic, however the probability setting doesn't seem to be  
> functioning.
> Thanks again for adding all these features,
> Dave

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