SUPCOMB, is a program to superimpose one 3D structure onto another. These structures can be low-resolution bead models and/or high resolution NMR or x-ray crystal structures. The alignment of shape models (ie. *.flm files) is not supported. There are two versions, supcomb13 and supcomb20. Supcomb13, the original algorithm, is quite slow but generates highly accurate superposition/alignment of structures. Supcomb20 is a modification of supcomb13 providing a more rapid superposition/alignment of structures, at the expense of accuracy.
The program represents each input structure as an ensemble of points, then minimizes a normalized spatial discrepancy (NSD) to find the best alignment of two models. NSD is a measure of quantitative similarity between sets of three-dimensional points and is calculated in the following way:
Briefly, if two three-dimensional models are represented as a set of points, for every point in the first set (model 1), the minimum value among the distances between this point and all points in the second set (model 2) is found, and the same is done for the points in the second set. These distances are added and normalized against the average distances between the neighboring points for the two sets.
For ideally superimposed similar objects, NSD tends to 0; it exceeds 1 if the objects systematically differ from one another.
Please refer to the paper cited above for further details about the implemented algorithm.
Running supcomb
Usage:
$> supcomb13 [[file1.pdb] [file2.pdb] [OPTIONS]]
or
$> supcomb20 [[file1.pdb] [file2.pdb] [OPTIONS]]