Well, this means that for example the variable $xC1 didn't get set to any value when you use it in line 80. Now lets look at the lines where you want to set the variable. It is in a part that is executed only when two if-clauses are true.

The warnings indicate that all variables that depend on the outer if-clause "if ($one[0]=~m/^HETATM/)" have the same problem. So this if-clause probably is never true for at least the first two executions of the outermost loop i.e. for the first two files (and it seems from your test output that there is a third file where the if-clause is successfully run through). Because of that the variables are empty and you get the warnings.

So you have to change your script so that when the information you seek is not in the file the rest of the loop isn't executed anymore.

For example: 

foreach $file (@one)
{
    my $allfound=0;
...
                   if ($one[2]eq "C4")
                        {
                          $allfound&=1;
                        $xC4=$one[6];
                        $yC4=$one[7];
                        $zC4=$one[8];
                        }

                        if ($one[2]eq "C1")
                        {
                        $allfound&=2;
                        $xC1=$one[6];
                        $yC1=$one[7];
                        $zC1=$one[8];
                        }

                        if ($one[2]eq "C13")
                        {
                        $allfound&=4;
                        $xC13=$one[6];
                        $yC13=$one[7];
                        $zC13=$one[8];
                        }
                }
        }
        close FILETWO;
        next if ($allfound!=7);

[download]

I'm using the first three bits in the variable $allfound to tell me if all if-clauses where run through at least once for this file.

In reply to Re^3: Hello im new to programming i need help by jethro
in thread Hello im new to programming i need help by fahadm89

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.