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.

Run DomainParser using defaults:
```
	domainparser 1atna.pdb
```
The 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).
Define the maximum number of domains (n):
```
	domainparser -md n 1atna.pdb
```
The 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.
Define the minimum number of residues (r) in a domain (default: r=40):
```
	domainparser -ml r 1atna.pdb
```
Define the two extremal points (residue numbers resid1 and resid2) for cutting one structure into two domains:
```
	domainparser -ex resid1 resid2 1atna.pdb
```
The 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.
Define number of sampling pairs (m) for extremal points (default: m=20):
```
	domainparser -sp m 1atna.pdb
```
Define the maximun number of beta-strands (b1) that allow to bridge two different domains (default: b1=1):
```
	domainparser -mbpass b1 1atna.pdb
```
Define the maximun number of hydrogen-bonding pairs (b2) across two different domains in a beta-sheet (default: b2=2):
```
	domainparser -mbpair b2 1atna.pdb
```
Define the minimum number of residues (k) per segment in a domain (default: k=35):
```
	domainparser -ms k 1atna.pdb
```
Some short segments may "dip" in and out of one domain while most of its flanks are in another domain, creating too many short segments in a domain. If such a segment has less than (s1) residues, it is reassigned to the domain which contains its flanks (default: s1=9):
```
	domainparser -mloop s1 1atna.pdb
```
A 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

Back to the DomainParser Page.