[Chimera-users] volume path tracer / render surface with marker set

Thomas Goddard goddard at cgl.ucsf.edu
Fri Feb 2 13:27:48 PST 2007

Hi Jeff,

  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 
features page.


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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