[Chimera-users] Question about molecular surface generation
Nihshanka Debroy
ndebroy at gmail.com
Wed Nov 15 00:14:00 PST 2006
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
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