domainer reads protein coordinate files and writes domains coordinate files.

Here is a sample session with domainer:

% domainer
Build domain coordinate files
Name of scop file for input (embl-like format) [Escop.dat]: /data/scop/Escop.dat
Location of coordinate files for input (embl-like format) [./]: /data/cpdb/
Location of coordinate files for output (embl-like format) [./]:
Extension of coordinate files (embl-like format) [.pxyz]:
Location of coordinate files for output (pdb format) [./]:
Extension of coordinate files (pdb format) [.ent]:
Name of log file for the embl-like format build [domainer.log1]: log.1
Name of log file for the pdb format build [domainer.log2]: log.2
D3SDHA_
D3SDHB_
D3HBIA_
D3HBIB_
D4SDHA_
D4SDHB_
D4HBIA_
D4HBIB_
D5HBIA_
D5HBIB_
D7HBIA_
D7HBIB_

Mandatory qualifiers:

-scop (infile)

Name of scop classification file (EMBL format input).

[-cpdb] (string)

Location of protein coordinate files (EMBL format input).

[-cpdbextn] (string)

Extension of coordinate files (EMBL format).

[-cpdbscop] (string)

Location of domain coordinate files (EMBL format output)

[-pdbscop] (string)

Location of domain coordinate files (PDB format output).

[-pdbextn] (string)

Extension of coordinate files (PDB format).

-cpdberrf (outfile)

Name of log file for the EMBL format build.

-pdberrf (outfile)

Name of log file for the PDB format build.