The ANALYSIS package contains a set of programs used to analyze structures or families of structures, typically from NMR-based calculations. Each analysis program performs a single geometric task:
program name what it does
ANGLES Calculate torsion angles and angle order parameters.
Optionally permutes degenerate atoms so that torsions
appear in "standard" torsion range.
AVESTR Calculate geometric mean structure.
DISCOM Calculate averate and RMS distance difference matrices
between corresponding atoms in two structure families.
DISTANCE Calculate average and rms distances, includes rm6
averaging or summation of equivalent protons
(can interpret pseudo-atom nomenclature).
HBONDS Calculate hydrogen bonds.
NOEVIO Calculate NOE distance constraint violations.
TORVIO torsion angle constraint violations
SUPER Superimpose structure onto another.
POSER Precision-weighted ensemble superposition.
EMPOSER Multiple ensemble precision-weighted superposition.
RMSCOM Compute average pairwise rms/residue within and
between two structure familes.
The DTAGS package (distributed beginning 971010, GAP 1.0) contains a set of programs used to perform systematic torsion angle grid search for polypeptide and polynucleotides structures, and to analyze properties of the resulting ensemble of structures.
reslib prepare input for search from primary sequence
and residue library
dtags correlated grid search in distance space for
linear submolecules.
newmol binary tree search in Cartesian space for
arbitrary branched molecules.
srchvec produce initial torsion vector spaces for newmol
launch (shell script/nawk program) prepare executable
script for large-scale binary tree search
spacecat "connecting" elements of binary tree search
spaceglue
spacejoin
spacenjoin
genave produce newmol input for generating distance average
and extrema matrices, and for embedding the average
distance structure.
genall produce newmol input for generating all structures
oriented to the average structure.
gengeo produce newmol input to analyze geometric properties
of structures (with option to oriented structures to to
the average structure, either in the lab frame or in a
local molecular frame)
The latest version of this package is 1.2.14, from September, 2006. You can download it here: