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 > -- > modeller-care@salilab.org http://www.salilab.org/**modeller/<http://www.salilab.org/modeller/> > Modeller mail list: https://salilab.org/mailman/**listinfo/modeller_usage<https://salilab.org/mailman/listinfo/modeller_usage> >