Ben,

Can you please clarify this for me:

1) I have a multi-chain PDB

2) I have a protein sequence that only matches against one of the chains in the PDB

So, how do I automatically, say using a python script and my protein sequence as a query, extract the chain ID of the PDB segment to which it matches? Is a script like that available in MODELLER? If so, can you please guide me to it. I have tried most of them but I cannot figure this one out.

The closest I came across is the "make_chains.py". But that only spits out all the possible chains in a PDB file into individual alignment files.

Thanks very much,

Amjad

On Mon, Oct 28, 2013 at 3:37 PM, Modeller Caretaker <modeller-care@salilab.org> wrote:

On 10/28/2013 12:01 PM, Amjad Farooq wrote:

For instance, if a PDB has 4 chains (say A, D, F, P) and I am interested
in extracting the chain ID of the second segment (D) that best aligns
with my query sequence, I do not believe you can extract that from PIR
alignment file, which only provides chain IDs of the first (A) and the
last chain (P).

No, but you can read in the corresponding PDB and extract the chains from that.

Ben Webb, Modeller Caretaker
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