How to Run DomainParser

The structure for partition needs to be prepared in the PDB format. In most cases, running DomainParser using defaults should give satisfactory partitions. However, several options offered in DomainParser can provide a partition that a user desires or correct some overcut/undercut partitions. Here, we use a PDB file 1atna.pdb as an example to show how to use the DomainParser program.

One can combine different options together in one command line, for example:

	domainparser -md 2 -mterm 15 -sp 8 -mbpass 0 1atna.pdb

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