osercinoglu / pdb2fasta

Take a PDB file and spit out protein sequence in 3 or 1 letter format

pdb2fasta

Current version 0.2

Take a PDB file and spit out protein sequence in 3 or 1 letter format.

Usage

pdb2fasta -f <pdbfile> [-c <chain>] [-t] 

Arguments

-f PDB file (required argument)

-c [optional] Defines the chain in PDB file to print (useful if a PDB file contains several proteins

-t [optional] Print three letter code instead of 1 letter code

-a [optional] Print the output in the CAMPARI sequence file format

Examples

Print all amino acid residues in the file with their one letter code

pdb2fasta -f file.pdb  

Print the number and names of the chains in the PDB file

pdb2fasta -c file.pdb 

Prints the amino acid residues in chain A in the PDB file

pdb2fasta -f file.pdb -c A 

Print the amino acid sequence, ignoring non-standard amino acids (DANGEROUS)

pdb2fasta -f file.pdb 2>/dev/null

About

This code was written by Alex Holehouse as part of the Pappu Lab. For more information contact [email protected]. For bug fixes please file a pull request.