[Chimera-users] volume path tracer / render surface with marker set
goddard at cgl.ucsf.edu
Fri Feb 2 13:27:48 PST 2007
There is no Chimera capability to create surfaces using marker
positions. Chimera can read three types of externally generated
surfaces: VRML, GRASP, and IMOD. The vrml and grasp readers are a
standard part of Chimera and the imod file reader is on the experimental
Some years ago I wrote Python code to stitch together loops created in a
program called PRIISM (used for light and electron microscopy) to form a
tubular surface. This was used to hand trace the nuclear envelope of
cells. It had no provision for giving the surface a thickness. It
created strips of triangles joining loops consisting of tens of points
in two parallel planes.
Interactive creation of surfaces would be useful for delimiting
membranes seen in EM tomography. I was asked about Chimera support for
this at a cellular tomography workshop in December. Programs for
segmenting em tomography all do this (IMOD, Analyze, ...) and I am not
decided on whether we should duplicate those capabilities in Chimera
given the many projects we have.
Karin Gross and Christoph Best at Max Planck Institute for
Biochemistry have been looking into making Chimera extensions to trace
EM tomography structures plane by plane.
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