[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:
http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/bild.html
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
releases.
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.
Best,
Elaine
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
http://www.cgl.ucsf.edu/home/meng/index.html
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