CCRXP ADV: User selected parameters for CCR identification

Choose a critereon to determine residue positions in space (from all atom coordinates to single atom position)
For calculating packing density: HELP
C-alpha atom Geometric center of all residue atoms

For clustering residues:HELP
C-alpha atom Geometric center of all residue atoms

Choose a distance critereon, at which residues will be included in packing density calculations and clustering
For calculating packing density (number of residues within the following distance):HELP
7A 8.0A 9.0 10.0

For clustering residues (two residues will be joined if they are closer than the following distance):HELP
4.0A 4.5A 5.0A 5.5A 6.0A 6.5A

Definition of residue contact with DNA (any to any atom distance) (has no effect for structures without DNA molecule).
3.0A 3.5A 4.0A 4.5A 5.0A 5.5A 6.0A 6.5A

Conservation score options: HELP
1. Maximum number of aligned sequences: HELP
20 50 100 150 200

Conservation score cutoff to include in clustering:
0.5 0.6 0.7 0.8 0.9

Other filtering options:
Include only exposed residues in clustering at following relative ASA cutoff (% exposed units): HELP
0 (include all residues) 10 20 30 40 50

Minimum number of residues in a cluster (clusters smaller than this will not be reported) HELP
1 2 3 4 5

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