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Chapter 4: Analysis Routines
• monitor nskip number statistics
• calc [ allinternals | sidechain ] resnumber resn atomname atna [ pdb file fname ]
• calc bond ( resnumber resn
atomname atna ) two times [ pdb file fname ]
• calc angle ( resnumber resn atomname atna )
• calc torsion ( resnumber resn atomname atna )
three times
four times
[ pdb file fname ]
[ pdb file fname ]
1. Arbitrary user-defined bonds, angles, or torsions are calculated between
any atoms (whether or not they follow the tree structure or are bonded).
2. All internal coordinates as defined in create (the tree structure) are
calculated.
These coordinates are calculated from atomic positions already existing
within an Impact job, or from a coordinate set read in from an external
PDB file.
4.1.3.1 Calc
Flag to calculate internal coordinates. If the calc option is chosen, multiple
bonds, angles, and torsions can be calculated within the same command
line. However one must quit from a measure session and call it again before
calc all or calc sidechain.
The calc all exactly calculates the internal coordinates as defined by the
tree, thus no improper dihedral angles will be calculated, and some desired
angles may also be missing.
When defining torsions be sure the order of the four atoms is the same as
the order used in the parameter file to define the desired torsional constant.
Else, the dihedral angles calculated will be for a different angle. (e.g. phi
(1, 2, 3, 4) is different from phi (1, 2, 4, 3) for atoms 1, 2, 3 and 4).
allinternals
calculate a list of all internal coordinates defined by the tree
structure in create.
bond
Calculates the distance between two atoms specified by two sets
of parameters: residue number; atom name. Atoms need not be
bonded.
angle
Calculates the angle between three atoms specified by three sets
of residue number; atom name parameters. Atoms need not be
bonded or follow tree structure.
torsion
Calculates the torsion angle between four atoms specified by four
sets of residue number; atom name parameters. Atoms need not
be bonded or follow tree structure.
sidechain
Calculates all torsions along side chain of the residue specified
by parameter resn, torsions follow tree structure.
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FirstDiscovery 3.0 Command Reference Manual