Hi,

I am new to perl, but I would like write a perl script that can convert xyz cordinates from a pdb file to distances using the formula:  
distance = SQRT[(X1-X2)^2  +  (Y1-Y2)^2 + (Z1-Z2)^2]

eg: line 1 xyz to line2 xyz
     line 1 xyz to line3 xyz
     line 1 to ...73
     line 2 to 3 and so on.

But I need to know which line to which line.
Any help would be so great and appreciated.

The pdb file format look like this
REMARK                                                              
ATOM        1  O1  VVA     1      20.542  18.415  14.035
ATOM        2  C2  VVA     1      21.588  17.620  14.671
ATOM        3  H3  VVA     1      21.893  18.095  15.605
ATOM        4  C4  VVA     1      22.849  17.597  13.752
ATOM        5  H5  VVA     1      22.659  16.957  12.887
ATOM        6  C6  VVA     1      23.208  19.009  13.227
ATOM        7  H7  VVA     1      22.404  19.424  12.617
ATOM        8  H8  VVA     1      23.407  19.695  14.054
ATOM        9  H9  VVA     1      24.101  18.970  12.600
ATOM     10  C10 VVA     1      24.078  17.043  14.513
ATOM     11 1H1  VVA     1      24.986  17.171  13.920
ATOM     12 2H1  VVA     1      24.223  17.571  15.458
ATOM     13 3H1  VVA     1      23.979  15.976  14.725
ATOM     14  C14 VVA     1      21.040  16.197  15.003
ATOM     15  H15 VVA     1      21.881  15.519  15.161
ATOM     16  C16 VVA     1      20.191  15.577  13.866
ATOM     17  H17 VVA     1      19.272  16.141  13.690
ATOM     18  H18 VVA     1      20.755  15.531  12.932
ATOM     19  H19 VVA     1      19.903  14.555  14.128
ATOM     20  C20 VVA     1      20.251  16.232  16.295
ATOM     21 1H2  VVA     1      19.164  16.223  16.236
ATOM     22  C22 VVA     1      20.938  16.240  17.456
ATOM     23 3H2  VVA     1      22.026  16.209  17.459
ATOM     24  C24 VVA     1      20.334  16.237  18.802
ATOM     25  O25 VVA     1      21.027  16.110  19.792
ATOM     26  N26 VVA     1      19.002  16.363  18.881
ATOM     27  H27 VVA     1      18.499  16.585  18.031
ATOM     28  C28 VVA     1      18.216  16.150  20.098
ATOM     29  H29 VVA     1      17.316  15.589  19.827
ATOM     30  H30 VVA     1      18.789  15.543  20.809
ATOM     31  C31 VVA     1      17.831  17.455  20.752
ATOM     32 2H3  VVA     1      18.521  18.288  20.656
ATOM     33  C33 VVA     1      16.697  17.496  21.476
ATOM     34  H34 VVA     1      16.082  16.598  21.541
ATOM     35  C35 VVA     1      16.202  18.631  22.258
ATOM     36  C36 VVA     1      14.930  18.374  23.045
ATOM     37  H37 VVA     1      14.504  17.389  22.841
ATOM     38  H38 VVA     1      15.118  18.425  24.120
ATOM     39  H39 VVA     1      14.160  19.107  22.799
ATOM     40  C40 VVA     1      16.857  19.811  22.304
ATOM     41 1H4  VVA     1      17.770  19.982  21.740
ATOM     42  C42 VVA     1      16.408  20.965  23.174
ATOM     43 3H4  VVA     1      15.564  20.703  23.820
ATOM     44  O44 VVA     1      17.518  21.298  23.996
ATOM     45  H45 VVA     1      17.779  20.471  24.446
ATOM     46  C46 VVA     1      16.044  22.195  22.332
ATOM     47  H47 VVA     1      15.935  23.063  22.985
ATOM     48 2H7  VVA     1      16.850  22.414  21.628
ATOM     49  C48 VVA     1      14.737  21.988  21.602
ATOM     50  O49 VVA     1      13.715  21.695  22.187
ATOM     51  C50 VVA     1      14.735  22.201  20.116
ATOM     52 1H5  VVA     1      15.288  23.110  19.879
ATOM     53 3H7  VVA     1      13.709  22.333  19.773
ATOM     54  C52 VVA     1      15.359  21.029  19.445
ATOM     55  O57 VVA     1      14.648  19.867  19.311
ATOM     56  C55 VVA     1      15.520  19.141  18.547
ATOM     57  H56 VVA     1      15.181  18.143  18.295
ATOM     58  N53 VVA     1      16.534  21.087  18.817
ATOM     59  C54 VVA     1      16.659  19.831  18.223
ATOM     60  C58 VVA     1      17.676  19.179  17.346
ATOM     61  O59 VVA     1      17.563  18.044  16.918
ATOM     62  N60 VVA     1      18.792  19.912  17.045
ATOM     63  C61 VVA     1      19.319  20.979  17.904
ATOM     64  H68 VVA     1      19.237  20.714  18.963
ATOM     65  H69 VVA     1      18.788  21.915  17.700
ATOM     66  C65 VVA     1      20.795  21.104  17.489
ATOM     67  H66 VVA     1      21.450  20.689  18.260
ATOM     68  H67 VVA     1      21.068  22.146  17.309
ATOM     69  C63 VVA     1      20.870  20.278  16.230
ATOM     70  H64 VVA     1      21.723  20.344  15.559
ATOM     71  C62 VVA     1      19.723  19.613  16.010
ATOM     72  C70 VVA     1      19.462  18.882  14.714
ATOM     73  O71 VVA     1      18.357  18.764  14.209
END





I've had a quick look at the desription of the .pdb format and it tells me that a CONECT record is used to specify which ATOMs are linked to which other ATOMs; I don't fully understand the data you've provided but I can't see that there's enough there for it to tell me this information.    Have you any CONECT or other records that might be of help?

I've looked at http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html to reseach CONECT ...

Your algorithm for the distances is correct, though you'd write sqrt in lower case, use round brackets, put $ characters in front of the variable names and use ** not ^ for "power of" in Perl.

$dist = sqrt(($x1-$x2)**2+($y1-$y2)**2+($z1-$z2)**2);

Hi Graham,

My PDB file does not have CONNECT information. I want to calculate NOE distances, which is the distance of 2 hydrogen atoms through space.
For eg: I would like to calculate the distance of H3 to H5; H3 to H7 and so on.

I have hundreds of PDB files with the same format, they just difference in XYZ coordinates. My aim is to write a perl script to calculate those specific H to H distances.

I am thinking about array, I think it is called 'list' in perl,  I need to name each XYZ cordinates of those H, so that the variable for the formula can be used. Am i right?

So what you really want is a parser to parse the ATOM lines in a pdb file, and store the data in a way, so as to be able to find it using the names in column 3?

So assuming column 3 names are all unique, which at a glance looks like they are, I would suggest a hash.

Hashes are like special arrays, but the index is a string, so can be something like H1, H2

Code:

use IO::File; my %atoms;       # Declare the hash my $fd=new IO::File( "yourfile.pdb" ); while( <$fd> ) {        chomp;                              # Strip line ending        my @rec=split(/\s+/);        # Split on white space        # Store X, Y and Z in the hash, indexed by col 3        # data is stored in an array reference        $atoms{ $rec[2] } = [ $rec[5], $rec[6], $rec[7] ]; } my $distance = your_distance_func(          $atoms{H1},        $atoms{H2} );

(incomplete and untested example)

You'll have to modify to get it to do what you want..

see:
       perldoc perlintro
       perldoc perldata
       perldoc perlreftut


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