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/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage