volume path tracer / render surface with marker set
hello, is there a way to render a surface of arbitrary thickness using a marker set? as in, fit some sort of spline to a marker set, with the constraint being that the algorithm assumes they all lie on the same surface? this would be useful for modeling membranes, perhaps it is already implemented and I am not seeing it in the dialogs. thanks, -J
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. http://www.cgl.ucsf.edu/chimera/experimental/experimental.html 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. Tom
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Jeff -
Thomas Goddard