We get a lot of questions like this one, of the form: "how can I use Perl to do something?" The short answer is, learn Perl - and then, you can use it to do anything.

What you are really asking is this. How can I use Perl to:

• open a file
• read it line by line
• identify specific text in each line
• print out the results

It doesn't matter that your file is a PDB file, or that you want to extract "HEADER". What you need to know are general Perl skills, which you can use as generalized solutions to many similar types of problem.

So first, learn the basics of file handling and regular expressions. Then, code like this will make perfect sense:

open FILE, "pdb275d.ent";
while(<FILE>) {
  chomp;
  my $line = $_;
  # print whatever comes after COMPND
  if ($line =~/^COMPND\s+(.*?)$/) {
    print "$1\n";
  }
}
close FILE;

Soon you will discover that if you have thought of a problem, it's likely that someone else did too and they created a solution. If you're lucky, that solution is something like the Bioperl project - a huge collection of libraries for processing biological data. In there you'll find Bio::Structure::IO for reading PDB files and Bio::Structure::Entry, for extracting information from them. But master the basics first.

Thanks a lot for ur help!!!as i am new to perl so learing it step by step... and one thing more i would like to know... If i have Number of files like 6000 pdb files how to extract same thing from all files an print in new file with filename and retrived information Thanks alot...i m highly obliged! Regards

hey thanks alot for help as i am new to perl and wass little confused... I want to ask if i wana extract same information for number of files like 6000 files and display in new file...how cn i do that?? Thanks a lot for ur help guys... Regards

hey thanks alot for help as i am new to perl and wass little confused... I want to ask if i want to extract same information for number of files like 6000 files and display in new file...how cn i do that?? Same information as above from odb file but for 6000 or so files and displat result in new file... Thanks a lot for ur help guys... Regards