1. use strict; !
2. There is no need for the @array variable, you can assign to a list of variables directly:

   @array=split(/-/,$value);
   $pdbid=$array[0];
   $from=$array[1];
   $to=$array[2];
   $chainid=$array[3];
   if($chainid eq "_")
   {
   $chainid=" ";
   }
   $menu1=$array[4];
   $menu2=$array[5];
   $menu3=$array[6];
   @array=();
   [download]

   is better written as

   ($pdbid, $from, $to, $chainid, $menu1, $menu2, $menu3) = split(/-/,$va
   +lue);
   if($chainid eq "_") {
     $chainid=" ";
   }
   [download]

3. You should find better names for the $menu1, $menu2 and $menu3 variables.
4. The rows of print statements are hard to read and completely unnecessary. Use qq{} or heredocs:

           print <<"*END*";
   select :$chainid
   wireframe on
   wireframe 70
   select :$chainid
   spacefill on
   select :$chainid
   spacefill 0.55
   select $from-$to:$chainid
   wireframe on
   wireframe 70
   select $from-$to:$chainid
   spacefill on
   select $from-$to:$chainid
   spacefill 0.55
   select $from-$to:$chainid
   color green
   *END*
   [download]

This looks as if it's made to run as a CGI, so the first thing I'd do is look in the web server's error log.

I'd also suggest that every open be followed with some variation of or die $! (I see one does have that, but others don't).

Check that the files you're expecting to be there really are there (if you die on open failure, that should make this problem obvious).

Note that Perl has a built-in chmod, so you don't have to use backticks. (And backticks in void context is frowned upon. Use system for that.)

I checked with this error_log file it is displaying nothing
[download]