I would like to extract one letter amino acid code from the PDB coordinate file.
•
written
by
skjobs1234 •
This can get you started, you can then modify it to suit your needs. Save it as get_pdb_aa.pl, and run with get_pdb_aa.pl < file.pdb > out.txt. This will output MMMMMLLLLLLLLKKKKKKKKKKKKKKK for the example you provided.
#!/usr/bin/env perl
use warnings;
use strict;
my %aa_table = (
ala => 'A',arg => 'R',asn => 'N',asp => 'D',
asx => 'B',cys => 'C',glu => 'E',gln => 'Q',
glx => 'Z',gly => 'G',his => 'H',ile => 'I',
leu => 'L',lys => 'K',met => 'M',phe => 'F',
pro => 'P',ser => 'S',thr => 'T',trp => 'W',
tyr => 'Y',val => 'V',
);
foreach my $line ( <STDIN> ) {
my ($v1, $aa, $v3) = unpack 'A17A3A60', $line;
print "$aa_table{ lc($aa) }";
}
can you tell me more, how unpack works in this case? and how it would be if the pdb file lines looks like this: ATOM 1 N N . MET A 1 1 ? 36.644 -24.949 8.853 1.00 29.12 ? 1 MET A N 1 ????????
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It would be helpful to paste an example PDB co-ordinate file. I'm not a Perl programmer, so, I won't provide an answer anyway, but it will help the other Perl programmers here.
And the expected output is? I guess for this example is
MLKKK, is that right? Or do you wantMMMMMLLLLLLL...?Why Perl? Usually, when we're addressing a bioinformatics problem, we look at the best tool for the job, not how to do something limiting ourselves to just one specific tool.
I found one more way.
See this site below:
http://www.ebi.ac.uk/pdbe-srv/PDBeXplore/sequence/
Insert a structure ID and/or the author surname:
http://www.ebi.ac.uk/pdbe/entry/pdb/1aa0/
Fetch sequence in the left bottom corner of the page:
VSGLNNAVQNLQVEIGNNSAGIKGQVVALNTLVNGTNPNGSTVEERGLTNSIKANETNIASVTQEVNTAKGNISSLQGDVQALQEAGYIPEAPRDGQAYVRKDGEWVLLSTFL
OR
Quick links (right upper corner)
• 1aa0 overview
http://www.ebi.ac.uk/pdbe/entry/pdb/1aa0/protein/1
Macromolecules:
There are several ways to find a sequence.