dsp2pdb: convert DSPACE .pdb files to Brookhaven or InsightII PDB format

Usage:

dsp2pdb input_file.pdb output_file.pdb

Description:

dsp2pdb takes a DSPACE .pdb file and converts it to Brookhaven or InsightII PDB format.

Complete original documentation:

 Usage:  "dsp2pdb [-bh] input_file output_file"

 The -b option ("Brookhaven style")
 suppresses the default behavior
 of appending an "n" to the first residue name,
 which is required for importing the files into
 the Biosym InsightII package.  This option will
 also allow you to transform files that have
 previously been changed using the defaults

 The -h option brings up a help screen giving
 the syntax for execution.

 This is a perl program to convert dspace PDB
 files to the standard Brookhaven
 format for PDB files, which is also the
 preferred format for MidasPlus
 and the required format for InsightII.


 Note:  If you are importing the file into
 InsightII, you must add hydrogens using
 the menu sequence:

 "Builder(or Biopolymer)/Modify/Hydrogens"

 before you can do minimization, annealing, etc.


 In order to add new amino acid substitutions
 from the definition of new residue types in
 dspace, go to the Substitute subroutine
 near line 230 of this file and add the new substitution
 pattern.  The format for Brookhaven PDB files is very
 strict as to position of the fields on a given line,
 so the number of characters in the new name must be
 equal to the number of characters in the old name,
 with the difference made up by spaces.
 For example, adding the line:

   s/ABCDE/DEF  /;

 would change the residue previously called ABCDE
 to one called DEF.  Note that the residue name should
 be left-justified in columns 18-20.