[Chimera-users] creating cubes and other 3D shapes

Elaine Meng meng at cgl.ucsf.edu
Fri Nov 18 12:22:18 PST 2005

Hi Stephen,
A recent addition to Chimera (version 1.2184 and later) is that it  
can read BILD format, a very simple text format for specifying lines,  
arrows, spheres, boxes, cones, and cylinders.  This sounds like what  
you are looking for.  The format description can be viewed at:


In release 1.2184 and snapshot 1.2186, there is a problem with  
transformations (translate, rotate, and scale commands in this  
format), but that is fixed in our working version, and thus in future  
It sounds like you may not want to use transformations anyway, just  
use the coordinate system of your protein. I've attached an example  
file that does not include any transformations.  This file can simply  
be opened in Chimera, for example with File... Open.

On Nov 18, 2005, at 10:48 AM, Stephen A. Smith wrote:

> Hi
> I want to create a cube (box; 1Å^3, 2Å^3, etc.) at specific grid  
> points
> and color them as needed.  Is this possible in Chimera?  It is easy to
> do with spheres by specifying an atom at the desired location and then
> defining its VDW radius.  I would like to create cubes and rectangles
> of various sizes, related to regions of my protein, to denote specific
> atomic / residue features.  Any help would be greatly appreciated.
> Thanks
> Steve

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

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