Damsup is a program that aligns a set of models with one model that is considered the most probable one (as obtained from damsel). Given a list of models in PDB format, the program superimposes them with the reference model by calling SUPCOMB (either SUPCOMB20 or SUPCOMB13, the latter of which is slower but more accurate, see Command-Line and Options). Damsup requires an input file containing the file names to be analyzed. The first file in the list is considered to be the reference model with which all other models will be aligned. During superposition, enantiomorphs are allowed and only CA atoms are used to compute an NSD (see damsel introduction). For DAMMIN or GASBOR averaging, 10-15 models are recommended. Maximum number of files is 50.
Running damsup
Usage:
$> damsup [[INPUTFILE] [OPTIONS]]