domainer

domainer

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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.