
Hi Chimera users, I have been generating molecular surfaces for several proteins and am hoping to perform some matrix calculations on the points where the surfaces are being calculated. So I was wondering if there is a way to reduce the # points where the surface is calculated/plotted, as that would really reduce the dimensions of my matrices! I am using the Delphi Controller to generate electrostatic potentials. My understanding of Delphi is that it finds finite difference solutions to the Poisson Boltzmann equation by mapping the system onto a grid of points. After the potentials are calculated at those grid points, when generating the potentials on the molecular surface, interpolation is used to calculate the potentials for locations on the molecular surface that are between points on the grid used in Delphi. So I don't think its the grid size for Delphi that I need to be reducing, but the # points where the actual molecular surface is calculated. Is it possible to reduce this number somewhere in the code files? Thanks a lot! Sincerely, Nihshanka

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. Tom
participants (2)
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Nihshanka Debroy
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Thomas Goddard