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

Thomas Goddard goddard at cgl.ucsf.edu
Fri Nov 18 20:38:58 PST 2005

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.


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"/>

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