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- create_BeadRep(selection='known and not PSEUDO', resolution=5, startNumBeads=2, mapTol=0.65, testGrad=False, verbose=False, writeMap=False, writePDB=False)
- Create a spherical bead representation of the atoms specified in the
selection argument. First, an atomic probability map is generated from
the specified selection using the atomProb.AtomProb facility with
grid spacing specified by the resolution argument. Then beads are added,
starting with startNumBeads. For a given number of beads, the position
and radius of each bead is varied such that the generated AtomProb map
matches as closely as possible the initial map generated by selection using
a gradient optimization scheme. If the cross-correlation coefficient of
the bead-generated map with the initial map is greater than the mapTol
argument, the procedure stops, otherwise the set of beads is discarded
and an increased number of beads in generated so that the minimization
process is repeated.
When mapTol is achieved, the bead atoms are created in the simulation
corresponding to selection. The return object contains a named tuple with
members beadAtoms, containing the created beads, and radii, containing
the optimized radii,
The created bead atoms' residue name and atom name are given by
the module-local variables resName, and name, which take default
value "bead" and "blob", respectivley. The segid takes the value Za,
where a is replaced by the number of times this function is called.
The chemType property is "Zb", where b is replaced by an index
corresponding to bead number. This so that unique radii can be assigned
by chemical type in the nonbonded term. We have found it useful to
multiply the radii by the factor 1.4 to best represent occupied regions
in a repelPot.RepelPot energy term.
Additional arguments are:
testGrad - this flag can be set to True to test the gradient in
the position/radius optimization procedure.
writeMap - set this to True to write out the atomProb,AtomProb
map associated with the bead representation in a file
named map-NUM.edm, where NUM is the number of beads.
writePDB - set this to True to write out the PDB associated with
the determined bead representation. In this PDB, the
radii are written to the B-factor PDB field in a file
named shape-NUM.pdb, where NUM is the number of beads.
verbose - If True, print information about the process of the
fitting procedure. Additional information printed for
integer verbose>1.
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