GAP (Geometric analysis programs) from G.P. Gippert.

The GAP (Geometric Analysis Programs) suite was written by Garry Gippert while he was at TSRI. GAP contains two separate program packages that were developed in parallel for the generation and analysis of structure ensembles. They use a common object library.

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:



Updated on June 21, 2017. Comments to case@biomaps.rutgers.edu