Hi everyone, I'm really sorry for my rookie mistakes I've only been programming a few months and am still learning, I've included my entire programme below, isolating areas of it would have made it too difficult to understand, please feel feel to just copy, paste and run, I will add my input word document; I've been using to my next post, you'll need to put it in a text document and then pass it to the perl programme as a command line argument (whatever the txt document is called) for it to run. again many thanks for all your help! regards Dan

#!C:\Perl\bin

$pdbfile=@ARGV[0];
open (PDB,$pdbfile);
@pdblines=<PDB>;
close (PDB);

($fixed, $moving, $interdomain, *atomcount, *atomtype, *resnum, *Axcoo
+rd, *Aycoord, *Azcoord, *Bxcoord, *Bycoord, *Bzcoord, $totalnumber) =
+ &informationretrieval(\@pdblines);

(*beginningfixed, *endingfixed, $nsegF) = &domainprocessing($fixed);

(*beginningmoving, *endingmoving, $nsegM) = &domainprocessing($moving)
+;

(*beginninginterdomain, *endinginterdomain) = &interdomainsort($interd
+omain); 

(*res_to_atom, *natres) = &restoatom(\@resnum, $totalnumber);

(*AMxcord, *AMycord, *AMzcord, *BMxcord, *BMycord, *BMzcord) = &coordi
+natesorter(\@Axcoord, \@Aycoord, \@Azcoord, \@Bxcoord, \@Bycoord, \@B
+zcoord, \@res_to_atom, \@natres, $nsegM, \@beginningmoving, \@endingm
+oving); 

#(*AFxcord, *AFycord, *AFzcord, *BFxcord, *BFxcord, *BFxcord) = &coord
+inatesorter(\@Axcoord, \@Aycoord, \@Azcoord, \@Bxcoord, \@Bycoord, \@
+Bzcoord, \@res_to_atom, \@natres, $nsegF, \@beginningfixed, \@endingf
+ixed); 

#($clashcounterA) = &calculation(\@AMxcord, \@AMycord, \@AMzcord, \@AF
+xcord, \@AFycord, \@AFzcord);

#($clashcounterB) = &calculation(\@BMxcord, \@BMxcord, \@BMxcord, \@BF
+xcord, \@BFxcord, \@BFxcord);

#print STDOUT $clashcounterA;

#print STDOUT $clashcounterB;

#####
#SUBROUTINES
#####

sub informationretrieval {

local ($pdblines) = @_;
my @atomcount;
my @atomtype; 
my @resnum;
my @chainID;
my @Axcoord;
my @Aycoord;
my @Azcoord;
my @Bxcoord;
my @Bycoord;
my @Bzcoord;

    #loops through pdb file
    foreach $pdblines(@pdblines) {
        
        #ignores co-ordinate information related to hindge
        if ($pdblines =~ /TER arrow molecule that represents hinge axi
+s for movement from conformer 1 to 2/) {

        last;
        }

    #fixed domain information retrieveal   
    $fixed = $pdblines[7];

    #moving domain information retrieveal
    $moving = $pdblines[10];

    #moving domain information retrieveal
    $interdomainA = $pdblines[19];
    $interdomainB = $pdblines[21];

    # processing of interdomain information
    $interdomainA .= ',';
    $interdomainA =~ s/select//;
    $interdomainA =~ s/\s//; 
    $interdomainA =~ s/-/,/g;
    $interdomainA =~ s/A//g;

    # processing of interdomain information
    $interdomainB =~ s/select//;
    $interdomainB =~ s/\s//; 
    $interdomainB =~ s/-/,/g;
    $interdomainB =~ s/A//g;

    $interdomain = $interdomainA . $interdomainB;

        # identifies atom information and saves atom number, residue n
+umber, chainID, X,Y,Z coordinates and atom type in separate arrays
        if ($pdblines =~ /^ATOM/) {
    
        $iat++;
        $atomcount[$iat]=substr($pdblines,7,4);
        $atomtype[$iat]=substr($pdblines,13,3); 
        $resnum[$iat]=substr($pdblines,22,4);
        $chainID[$iat]=substr($pdblines,21,1);
    
            if ($chainID[$iat] eq 'A') {
            
            $Axcoord[$iat] = substr($pdblines,30,8);
            $Aycoord[$iat] = substr($pdblines,38,8);
            $Azcoord[$iat] = substr($pdblines,46,8);

            }

            elsif ($chainID[$iat] eq 'B') {

            $Bxcoord[$iat] = substr($pdblines,30,8);
            $Bycoord[$iat] = substr($pdblines,38,8);
            $Bzcoord[$iat] = substr($pdblines,46,8);

            }
        }
    }

return ($fixed, $moving, $interdomain, \@atomcount, \@atomtype, \@resn
+um, \@Axcoord, \@Aycoord, \@Azcoord, \@Bxcoord, \@Bycoord, \@Bzcoord,
+ $iat);

}

sub domainprocessing {

local ($domain) = @_;
my @beginningdomain;
my @endingdomain;
@domainnumbers;
my $nseg;

    # processing of domain information
    $domain =~ s/select//;
    $domain =~ s/\s//; 
    $domain =~ s/-/,/g;
    $domain =~ s/A//g;

    # split domain information into an array
    @domainnumbers = split(/,/, $domain);

    $nseg = @domainnumbers/2;

        # divide domain information into beginning and ending regions 
+of the domains         
        foreach $domainnumbers (@domainnumbers) {
               
            # if array entry is divisable by 2 (even numbered) then it
+ is put in the beginning array
            if ($i % 2 == 0) {
            $ibeg++;
            $beginningdomain[$ibeg] = $domainnumbers[$i];

            }  
        
            # if array entry is not divisable by 2 (odd numbered) then
+ it is put in the ending array
               elsif ($i % 2 != 0) {
            $iend++;
            $endingdomain[$iend] = $domainnumbers[$i];
               }
        
            # print error if something goes wrong 
               else {
                print STDOUT 'Error'; 
               }

            $i++;
        }

$ibeg = 0;
$iend = 0;
$i = 0;

return (\@beginningdomain, \@endingdomain, $nseg);
}

    
sub interdomainsort {
    
local ($interdomain) = @_;
my @interdomainnumbers;
my @beginninginterdomainunsorted;
my @endinginterdomainunsorted;

# split interdomain information into an array
@interdomainnumbers = split(/,/, $interdomain);

    # divide domain information into beginning and ending regions of t
+he domains     
    foreach $interdomainnumbers (@interdomainnumbers) {
       
        # if array entry is divisable by 2 (even numbered) then it is 
+put in the beginning array
        if ($e % 2 == 0) {
        $kbeg++;
        $beginninginterdomainunsorted[$kbeg]= $interdomainnumbers[$e];
        }
  
        # if array entry is not divisable by 2 (odd numbered) then it 
+is put in the ending array
           elsif ($e % 2 != 0) {
        $kend++;
        $endinginterdomainunsorted[$kend]= $interdomainnumbers[$e];
        }
       
        # print error if something goes wrong
        else {
         print STDOUT 'Error'; 
         }

        $e++;
    }

$kbeg = 0;
$kend = 0;
$e = 0;

@beginninginterdomain = sort @beginninginterdomainunsorted; 
@endinginterdomain = sort @endinginterdomainunsorted;

return (\@beginninginterdomain, \@endinginterdomain);

}

sub restoatom {

local ($resnum, $totalnumber)= @_;
my $iatres;
my @natres;
my @res_to_atom;

    #sorting residue to atom number
    $iatres=0;

    $resnum[0]=$resnum[1];

    for ($iat=1; $iat<=$totalnumber; $iat++) {

        #if atom is in the same amino acid
        if ($resnum[$iat] == $resnum[$iat-1]) {
        
        $iatres++;
        $res_to_atom[$resnum[$iat]][$iatres] = $iat;
        }

        #else if atom is in different amino acid
        else {

        $natres[$resnum[$iat-1]] = $iatres;
        $iatres = 1;
        $res_to_atom[$resnum[$iat]][$iatres] = $iat;
        }
    }

return (\@res_to_atom, \@natres);
}

#Sorts through moving coordinate information for calculation
sub coordinatesorter {

local (*Axcoord, *Aycoord, *Azcoord, *Bxcoord, *Bycoord, *Bzcoord, *re
+s_to_atom, *natres, $nseg, *beginning, *ending) = @_;

my @Axcord;
my @Aycord;
my @Azcord;
my @Bxcord;
my @Bycord;
my @Bzcord;
#my $interdomaincounter=1;
my $counter = 0;

    for ($iseg = 1; $iseg <= $nseg; ++$iseg){

        for ($ires = $beginning[$iseg]; $ires <= $ending[$iseg]; ++$ir
+es) {

                for ($iat = 1; $iat <= $natres[$ires]; ++$iat) {

                $Axcord->[$counter] = $Axcoord[$res_to_atom[$ires][$ia
+t]];
                $Aycord->[$counter] = $Aycoord[$res_to_atom[$ires][$ia
+t]];
                $Azcord->[$counter] = $Azcoord[$res_to_atom[$ires][$ia
+t]];
                $Bxcord->[$counter] = $Bxcoord[$res_to_atom[$ires][$ia
+t]];
                $Bycord->[$counter] = $Bycoord[$res_to_atom[$ires][$ia
+t]];
                $Bzcord->[$counter] = $Bzcoord[$res_to_atom[$ires][$ia
+t]];

print STDOUT $Axcord[$counter];

            $counter++;

            }
        }
    }

print STDOUT "should print out @Axcord array but does'nt?!", @Axcord;
return (\@Axcord, \@Aycord, \@Azcord, \@Bxcord, \@Bycord, \@Bzcord);

}

#Distance Calculation
sub calculation {            

local ($Mxcoord, $Mycoord, $Mzcoord, $Fxcoord, $Fycoord, $Fzcoord) = @
+_;

my $fixedcoordsize = @Fxcoord; 
my $movingcoordsize = @Mxcoord;
my $clashcounter;

    for($M=1; $M <= $fixedcoordsize; $M++){
   
        for($F=1; $F <= $movingcoordsize; $F++){

        $distance[$F] = sqrt(($Mxcoord[$F] - $Fxcoord[$M])**2 + ($Myco
+ord[$F] - $Fycoord[$M])**2 + ($Mzcoord[$F] - $Fzcoord[$M])**2);      
   
            if ($distance[$F] <= 4) {

            $clashcounter++;
            #print STDOUT "$atomtype[$F]";
            #print STDOUT "$resnum[$F]";
            #print STDOUT "$atomcount[$F]\n"; 
            }
            }
    }

return ($clashcounter);
}
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