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Miscellaneous rules and features
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MODELLER A Program for
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Contents
Index
M
ODELLER
general reference
Sections in this Chapter describe technical aspects of M
ODELLER
.
Subsections
Miscellaneous rules and features of M
ODELLER
M
ODELLER
system
Controlling breakpoints and the amount of output
File naming
Environment variables
Reading or writing files
Coordinate files and derivative data
File types
Stereochemical parameters and molecular topology
Modeling residues with non-existing or incomplete entries in the topology and parameter libraries
Residues with defined topology, but with missing parameters
Block (BLK) residues with undefined topology and parameters
Spatial restraints
Specification of restraints
Static and dynamic restraints
Feature types
Mathematical forms of restraints
Restraint violations
Specification of pseudo atoms
Excluded pairs
Rigid bodies
Symmetry restraints
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