Damsel is a program that compares a set of models, finds the most probable one and outliers (uses SUPCOMB). Given several structures in PDB format, the program superimposes all possible pairs by calling SUPCOMB (either SUPCOMB20 or SUPCOMB13, the latter of which is slower but more accurate, see Command-Line and Options). It then writes a table to select the most probable structure and to discard most divergent models. This table contains the values of agreement between the pairs of models and also the average agreement for each model with the others. The agreement is expressed in terms of a normalized spatial discrepancy ( NSD, see also Kozin & Svergun (2001). Automated matching of high- and low-resolution structural models. J. Appl. Cryst. 34, 33). During superposition, enantiomorphs are allowed and only CA atoms are used to compute the NSD. The model with the lowest average NSD is considered the most probable one, those with the highest NSDs are considered outliers. The table is written to the file damsel.log, which can be further used as input for damsup (see damsel output files)
NOTE: For DAMMIN or GASBOR averaging, 10 models are recommended. The maximum number of input models is 50. Models whose NSD exceeds 2 standard deviations from the mean are considered outliers.
Running damsel
Usage:
$> damsel [[INPUTFILE] [OPTIONS]]