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
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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@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
Hi Steve,
The Chimera volume path tracer tool can place markers which are spheres and connect them with cylinders. The spheres and cylinders can be made of small radius to make the outline of a cube.
Below is an example XML file that makes a cube positioned at the origin with side length 1. You can change the x, y, z values to put it where you want it. When you open it in Chimera it will create a molecule model (it is implemented as atoms and bonds) and you can adjust its color, or move it relative to other models as you like.
Tom
--- File cube.cmm follows. Use the ".cmm" suffix so it is recognized by Chimera.
<marker_set name="cube"> <marker id="1" x="0" y="0" z="0" radius="0.1"/> <marker id="2" x="1" y="0" z="0" radius="0.1"/> <marker id="3" x="0" y="1" z="0" radius="0.1"/> <marker id="4" x="1" y="1" z="0" radius="0.1"/> <marker id="5" x="0" y="0" z="1" radius="0.1"/> <marker id="6" x="1" y="0" z="1" radius="0.1"/> <marker id="7" x="0" y="1" z="1" radius="0.1"/> <marker id="8" x="1" y="1" z="1" radius="0.1"/> <link id1="1" id2="2" radius="0.1"/> <link id1="2" id2="4" radius="0.1"/> <link id1="4" id2="3" radius="0.1"/> <link id1="3" id2="1" radius="0.1"/> <link id1="5" id2="6" radius="0.1"/> <link id1="6" id2="8" radius="0.1"/> <link id1="8" id2="7" radius="0.1"/> <link id1="7" id2="5" radius="0.1"/> <link id1="1" id2="5" radius="0.1"/> <link id1="2" id2="6" radius="0.1"/> <link id1="3" id2="7" radius="0.1"/> <link id1="4" id2="8" radius="0.1"/> </marker_set>
participants (3)
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Elaine Meng -
Stephen A. Smith -
Thomas Goddard