Re: Rearrange the residue number of a pdb file according to the residues names

On the face of it, your problem is easily solved with Perl. You just need a little help with the jargon.

use strict;
use warnings;
[download]

...would show you that $m51 is not defined on line 39. This is probably a typo -- please use real code :D.

It is not clear what the script should be doing, other than rewriting all the ATOM lines, without field 4.

This snippet (reformatted for "standard" readability):

foreach $line (@m3,@m5){
    if ($m3[$line] eq $m3[$line+1]) {
        $m5[i]=$m5[i+1];
    } elsif ($m3[$line] ne $m3[$line+1]) {
        $m5[i+1]=$m5[i]+1;
    }
}
[download]

...tries to index @m3 by using one of its values. According to your regex, $m3 is \w{3}, so it will probably evaluate to index 0. Also, using "i" as an index should not compile.

Please show us your sample script, and a sample input and output (what you got, and what you really want). We can then walk you through this.

-QM
--
Quantum Mechanics: The dreams stuff is made of

Comment on Re: Rearrange the residue number of a pdb file according to the residues names Select or Download Code

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Re^2: Rearrange the residue number of a pdb file according to the residues names by nastaziales (Initiate) on Jun 18, 2015 at 12:42 UTC
ATOM 310 1HH2 ARG A 607 -31.278 29.882 25.723 1.00 99.99 ATOM 311 2HH2 ARG A 607 -32.344 30.932 24.851 1.00 99.99 ATOM 312 N LEU A 608 -36.327 31.914 18.187 1.00 65.62 ATOM 313 CA LEU A 608 -37.435 32.634 17.559 1.00 67.47 ATOM 314 C LEU A 608 -38.434 33.052 18.624 1.00 74.29 ATOM 315 O LEU A 608 -38.982 32.201 19.331 1.00 71.12 ATOM 316 CB LEU A 608 -38.110 31.803 16.459 1.00 64.64 ATOM 317 CG LEU A 608 -39.261 32.481 15.719 1.00 71.07 ATOM 318 CD1 LEU A 608 -38.782 33.704 14.929 1.00 73.68 ATOM 319 CD2 LEU A 608 -39.981 31.498 14.829 1.00 69.63 ATOM 320 H LEU A 608 -36.638 31.041 18.563 1.00 99.99 ATOM 321 N ARG A 565 -38.634 34.587 18.911 1.00 22.27 ATOM 322 CA ARG A 565 -39.655 35.200 19.766 1.00 23.04 ATOM 323 C ARG A 565 -40.963 35.104 19.007 1.00 22.72 ATOM 324 O ARG A 565 -41.046 35.500 17.847 1.00 24.21 ATOM 325 CB ARG A 565 -39.275 36.643 20.105 1.00 99.99 ATOM 326 CG ARG A 565 -38.044 36.770 20.986 1.00 99.99 [download] This is an input example, the 4th column is the residue name and the 6th the residue number, in the input there is a discontinuity in the residue number, when the residue name changes the residue number should be the previous residue number plus 1, so i need a script that will take a pdb file with discontinuities and will give a pdb file with the same format but with a continuous res number	[reply] [d/l]
Re^3: Rearrange the residue number of a pdb file according to the residues names by QM (Parson) on Jun 18, 2015 at 13:38 UTC
I need a script that will take a pdb file with discontinuities and will give a pdb file with the same format but with a continuous res number I'm assuming here that every time the residue name changes, the residue number is incremented. And in fact, that later on, the same residue name may occur again (with some intervening lines with different residue names), but should have a different number. I would rework your original script to something like this. #!/usr/bin/env perl # Read a PDB file and change the residue numbers to be continuous. use strict; use warnings; print "\nEnter the PDB input file: "; my $inputFile = <STDIN>; chomp $inputFile; unless (open(INPUTFILE, "<", $inputFile)) { die "Cannot read from <$inputFile>, $!"; } my $output_file = "my2pdb.txt"; open(PDBOUT,">>my2pdb.txt") or die "Cannot open <$output_file> for writing, $!"; my $last_residue_name = ''; my $last_residue_number = 0; while (<INPUTFILE>) { if (m/^ATOM/) { my @m = split; # Increment the residue number if the residue name changes if ($m[3] eq $last_residue_name) { $m[5] = $last_residue_number; } else { $m[5] = ++$last_residue_number; $last_residue_name = $m[3]; } printf PDBOUT "%4s %5s %4s %3s %1s %4s %7s %7s %7s %6s %6s +\n", @m; } } exit; [download] Here's the input file I used: ATOM 310 1HH2 ARG A 607 -31.278 29.882 25.723 1.00 99.99 ATOM 311 2HH2 ARG A 607 -32.344 30.932 24.851 1.00 99.99 ATOM 312 N LEU A 608 -36.327 31.914 18.187 1.00 65.62 ATOM 313 CA LEU A 608 -37.435 32.634 17.559 1.00 67.47 ATOM 314 C LEU A 608 -38.434 33.052 18.624 1.00 74.29 ATOM 315 O LEU A 608 -38.982 32.201 19.331 1.00 71.12 ATOM 316 CB LEU A 608 -38.110 31.803 16.459 1.00 64.64 ATOM 317 CG LEU A 608 -39.261 32.481 15.719 1.00 71.07 ATOM 318 CD1 LEU A 608 -38.782 33.704 14.929 1.00 73.68 ATOM 319 CD2 LEU A 608 -39.981 31.498 14.829 1.00 69.63 ATOM 320 H LEU A 608 -36.638 31.041 18.563 1.00 99.99 ATOM 321 N ARG A 565 -38.634 34.587 18.911 1.00 22.27 ATOM 322 CA ARG A 565 -39.655 35.200 19.766 1.00 23.04 ATOM 323 C ARG A 565 -40.963 35.104 19.007 1.00 22.72 ATOM 324 O ARG A 565 -41.046 35.500 17.847 1.00 24.21 ATOM 325 CB ARG A 565 -39.275 36.643 20.105 1.00 99.99 ATOM 326 CG ARG A 565 -38.044 36.770 20.986 1.00 99.99 [download] And here's the output I got (note that column 5 is included, unlike your initial example): ATOM 310 1HH2 ARG A 1 -31.278 29.882 25.723 1.00 99.99 ATOM 311 2HH2 ARG A 1 -32.344 30.932 24.851 1.00 99.99 ATOM 312 N LEU A 2 -36.327 31.914 18.187 1.00 65.62 ATOM 313 CA LEU A 2 -37.435 32.634 17.559 1.00 67.47 ATOM 314 C LEU A 2 -38.434 33.052 18.624 1.00 74.29 ATOM 315 O LEU A 2 -38.982 32.201 19.331 1.00 71.12 ATOM 316 CB LEU A 2 -38.110 31.803 16.459 1.00 64.64 ATOM 317 CG LEU A 2 -39.261 32.481 15.719 1.00 71.07 ATOM 318 CD1 LEU A 2 -38.782 33.704 14.929 1.00 73.68 ATOM 319 CD2 LEU A 2 -39.981 31.498 14.829 1.00 69.63 ATOM 320 H LEU A 2 -36.638 31.041 18.563 1.00 99.99 ATOM 321 N ARG A 3 -38.634 34.587 18.911 1.00 22.27 ATOM 322 CA ARG A 3 -39.655 35.200 19.766 1.00 23.04 ATOM 323 C ARG A 3 -40.963 35.104 19.007 1.00 22.72 ATOM 324 O ARG A 3 -41.046 35.500 17.847 1.00 24.21 ATOM 325 CB ARG A 3 -39.275 36.643 20.105 1.00 99.99 ATOM 326 CG ARG A 3 -38.044 36.770 20.986 1.00 99.99 [download] (I don't do formats, you'll have to figure that out for yourself.) Now that still begs the question of whether you wanted the entire input file written to the output, or just the ATOM section. I'm assuming I've missed several hints about the final output, but this is the basic structure. -QM -- Quantum Mechanics: The dreams stuff is made of	[reply] [d/l] [select]
Re^4: Rearrange the residue number of a pdb file according to the residues names by nastaziales (Initiate) on Jun 18, 2015 at 18:04 UTC
Thank you very much it works great !!	[reply]