FASTA and PDB: How to specify chain? For proteins that have multiple chains (e.g., 1EMS), is there an easy way to specify which chain I want to use for blastp?
I cannot imagine that I am the first person to have this problem, but so far my only solution has been to write my own script that gets the chain I want from the .pdb file and convert that to a .fasta file.
The NCBI BLAST can be used with the PDB DB (which NCBI has). The PDB codes are stored as 4 letter codes underscore chain, e.g. 1GFL_B. The catch is segment identifiers —but generally they are the same peptide so shouldn't be an issue.
You can search specifically the PDB DB in NCBI (not the RCSB PDB) by setting the database to PDB.