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Calculation of residue depth (using Michel Sanner's MSMS program for the
surface calculation).
Residue depth is the average distance of the atoms of a residue from
the solvent accessible surface.
Residue Depth:
rd=ResidueDepth(model, pdb_file)
print rd[(chain_id, res_id)]
Direct MSMS interface:
Typical use:
surface=get_surface("1FAT.pdb")
Surface is a Numeric array with all the surface
vertices.
Distance to surface:
dist=min_dist(coord, surface)
where coord is the coord of an atom within the volume
bound by the surface (ie. atom depth).
To calculate the residue depth (average atom depth
of the atoms in a residue):
rd=residue_depth(residue, surface)
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ResidueDepth Calculate residue and CA depth for all residues. |
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standard_aa_names =
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to_one_letter_code =
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Return a Numeric array that represents the vertex list of the molecular surface. PDB_TO_XYZR --- pdb_to_xyzr executable (arg. to os.system) MSMS --- msms executable (arg. to os.system) |
Return average distance to surface for all atoms in a residue, ie. the residue depth. |
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standard_aa_names
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to_one_letter_code
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