domainparser 1atna.pdbThe output shows the partition for each domain in terms of ranges of residue numbers:
4 domains have been found for 1atna: Domain 1 : 34-96. Domain 2 : 181-272. Domain 3 : 148-180; 273-336. Domain 4 : 0-33; 97-147; 337-372.The program also generates a new file 1atna_dom.pdb, with the "temperature factor" column (column 61-66 of an "ATOM" entry) showing domain numbers. A user can display domains in different colors with the option of "color by temperature factor" in a molecular viewer program (e.g., RasMol, Insight, and VMD).
domainparser -md n 1atna.pdbThe followins is the result for n=2, i.e., cutting 1atna.pdb into 2 domains:
2 domains have been found for 1atna: Domain 1 : 0-147; 337-372. Domain 2 : 148-336.This option can be used for a less detailed partition.
domainparser -ml r 1atna.pdb
domainparser -ex resid1 resid2 1atna.pdbThe two extremal points are two initial seeds potentially in two different domains. The default combines several options to sample extremal points, including using two points that are farthest away from each other in the structure.
domainparser -sp m 1atna.pdb
domainparser -mbpass b1 1atna.pdb
domainparser -mbpair b2 1atna.pdb
domainparser -ms k 1atna.pdb
domainparser -mloop s1 1atna.pdbA similar rule is applied to a segment at the terminus of a protein sequence and with less than (s2) residues in the domain (default: s2=9):
domainparser -mterm s2 1atna.pdb
One can combine different options together in one command line, for example:
domainparser -md 2 -mterm 15 -sp 8 -mbpass 0 1atna.pdb