[modeller_usage] Fwd: Extract Chain ID

I am not scanning against PDB95 but rather working on multi-chain PDBs locally.

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).

Also, how would I know if my query sequence aligned up against chain D unless I look at the alignment file manually. I want to automate this procedure. In other words, have a python script extract the chain ID of the aligned segment in a multi-chain PDB and automatically proceed to next step for homology modeling--that is I only want to use segment D as a template during homology modeling rather than the whole multi-chain PDB, which compromises the quality of the alignment and hence the model.

Thanks!

On Mon, Oct 28, 2013 at 2:36 PM, Modeller Caretaker <" target="_blank">> wrote:

On 10/27/2013 11:08 AM, Amjad Farooq wrote:

Is it possible to perform an automatic search of a multi-chain PDB
template with a known protein sequence that is to be modeled (say
100-200 residues in length) and then extract the chain ID of the segment
of the PDB template that best matches with the query sequence.

If I understand you correctly, this is straightforward. If you're scanning against our PDB95 database, for example, all the templates are single chain, and the chain ID is simply the last character in the align code.

If you're trying to align against a multi-chain template (presumably a local alignment) you could extract the chain ID trivially from the alignment object.

Ben Webb, Modeller Caretaker
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