February 27, 2007
This tool allows selecting surface pieces, coloring them, and measuring their enclosed volume and surface area. The surface pieces are the connected components of a volume contour surface. Use menu entry
Tools / Volume Data / Pick Surface Pieces
to show the dialog.
Image shows a single contour surface of a chaperonin EM density map (EMD 1046). Each piece was selected by clicking the mouse ctrl-button-3. Different colors were chosen in the Pick Surface Pieces dialog before picking each piece.
The coloring is lost if you change the contour threshold level in Volume Viewer.
The volume is the exact volume enclosed by the triangulated surface. If the surface has a hole (because it intersects the boundary of the volume brick) then the volume is not computed. You can use the zero boundary accelerator zb (turn on accelerators with menu entry Tools / General Controls / Accelerators On and type zb in the graphics window) to close the boundary holes. The zero boundary command is described in the Volume Eraser documentation.
February 27, 2007.
Updated for Chimera version 1.2348 which uses NumPy instead of Numeric Python.
September 5, 2006.
Added calculation of surface area for picked surface piece. Moved calculations of surface intercept, connected surface component, volume and surface area from Python to C++ to increase execution speed.
December 21, 2005.
Developed for Manfred Auer to measure volumes of pieces of EM tomograms.