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SUPCOMB

Superimposes one 3D structure onto another. These structures can be low-resolution bead models and/or high resolution NMR or X-ray crystal structures.

Versions 2.3 © ATSAS team 1999-2013

Written by M.B. Kozin1,2, M.V. Petoukhov1, D. Franke1 & D.I. Svergun1
1European Molecular Biology Laboratory, Hamburg Outstation
EMBL c/o DESY
Notkestrasse 85, Geb. 25a
22603 Hamburg
Germany
2Institute of Crystallography
Russian Academy of Sciences
Leninsky pr. 59
119333 Moscow
Russia

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.

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.

If you use SUPCOMB in your work, please cite:
M.Kozin & D.Svergun (2001) Automated matching of high- and low-resolution structural models J Appl Cryst. 34, 33-41.


  Last modified: March 7, 2014

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