[Chimera-users] Question about molecular surface generation

Thomas Goddard goddard at cgl.ucsf.edu
Wed Nov 15 09:10:30 PST 2006

Hi Nihshanka,

  There is a parameter called "vertex density" that can be adjusted when
computing a molecular surface in Chimera.  Open a PDB model, use menu
entry Actions / Surface / show, open Model Panel with menu entry
Favorites / Model Panel, double click on the MSMS surface listed in
Model Panel to get the surface attributes dialog.  Then change the
vertex density value (default 2) and press the Enter key to recalculate
the surface.  To see how many points you are getting change the
"representation" setting in the attributes dialog to "mesh".  I believe
the vertex density means points per square angstrom.

  This method can reduce the number of surface points to a few per
atom at the surface.  If you want fewer points than that then other
techniques would be needed involving writing Python code to sample the
mesh of points more coarsely.


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