#!/usr/bin/perl

# template file for reading in pdb file and performing some operation
# on one of the columns of data and then writing it back out.
# For example, to change chainid, or renumber AA sequence, etc.

while (<STDIN>) {        # loop over input lines

    $keyword = substr($_,0,6);    # look for ATOM record
    if ($keyword eq "ATOM  ") {

        # dissect line into parts
        chop;
        $num = substr($_,6,5);
        $atom = substr($_,12,4);
        $res = substr($_,17,3);
        $chainid = substr($_,21,1);
        $resn = substr($_,22,4);
        $xcor = substr($_,30,8);
        $ycor = substr($_,38,8);
        $zcor = substr($_,46,8);
        $occ = substr($_,54,6);
        $bfac = substr($_,60,6);
        $segid = substr($_,72,4);
        $elm = substr($_,76,2);
        $charge = substr($_,78,2);

        # do whatever we want with different fields


        # print ATOM line
        printf "ATOM  %5d %4s %3s %1s%4d    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
                $num,$atom,$res,$chainid,$resn,$xcor,$ycor,$zcor,$occ,$bfac,$segid,$elm,$charge;
        }

    # not ATOM record so print whatever we find there
    else {
        print $_;
        }

    # end of while loop
    }