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