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MonZop / BioBlender

AddOn for Blender to do molecular work
BSD 2-Clause "Simplified" License
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Packages Used #19

Open zeffii opened 9 years ago

zeffii commented 9 years ago

WIP

As part of getting to know BioBlender here follows a summary of packages (python or executables) currently used by BioBlender2, and the functionality that these packages facilitate.

Package Function
PyMOL calculates the Connolly Surface, or Solvent excluded surface (SES)
which delimits the space of the molecule.
It outputs a .wrl file , BB imports this and makes a triangulated surface mesh and vertex_color_map.
- install pyMOL from source (windows)
- install pyMOL from source (linux)
pyMLP Molecular Lipophilicity Potential evaluator
pyMLP produces a [.dx map file]() from a .pdb file.
BB .pdb > pyMLP .dx
apbs Adaptive Poisson-Boltzmann Solver
calculates the Electrostatic Potential (EP)
website requests registration (to help future grants)
http://sourceforge.net/projects/apbs/files/apbs/apbs-1.4.1/ (apbs installers)
MonZop commented 9 years ago

PyMOL is used to calculate the Connolly Surface, or Solvent excluded surface (SES), which delimits the space of the molecule. It outputs a .wrl file of the mesh

MonZop commented 9 years ago

To obtain a vertex color map, BB uses the mesh generated by pyMOL: each vertex of the mesh gets a value obtained by trilinear interpolation of the values in the grid. I have no idea of where this operation is coded :(