After Extracting The Primary Structure Of A Multi-Chain Protein From Its Pdb File, How To Display In Fasta Format??

Question

[Coli]

After extracting the primary structure of a multi-chain protein from its PDB file cannot find a way to display it in FASTA format?? If the pdb text file has only one chain is pretty easy to put all the info in a here document and print staff on the screen as well as storing the same output in file.

However if you have more than one chain in the pdb file I can get the desired chains with each chain letter and length of each chain as well and print the info on the screen while iterating with a loop to get each chain. How do I send this output in a file that I wanna create?? with one chain u simply do:

my $fasta =<<FASTA;
>$id|$title|$chain_length aa
$sequence
FASTA
print $fasta;

How you do that when you have multiple chain and you need to display one chain at a time in a fasta format??????

[Neilfws]

Why did you (only) tag this question 'bioperl'? Do you want to use Bioperl to solve the problem? There is no mention of it in your question.

[Neilfws]

Also, I reformatted your code, but it does not make much sense. Perhaps you could edit it to show what you are trying to achieve. Lines with code need 4 leading spaces and blank lines top and bottom.

Answer 1

[Neilfws]

Some (mostly non-coding) solutions to this problem are discussed in this blog post at the P212121 blog.

The simplest is probably to use the direct FASTA download from the PDB. For example, to get PDB code 4HHB, chain A:

curl -o 4HHBA.fa "http://www.rcsb.org/pdb/download/downloadFile.do?fileFormat=fastachain&compression=NO&structureId=4HHB&chainId=A"

Answer 2

[bluewoodtree]

It might be a little bit late, but if someone is still looking for a solution: I wrote a web app for that:

http://bluewoodtree.zxq.net/pdb_to_fasta.html