Dear Community, I am looking for a tool that can convert a potential MR search model to match the residue number and a.a. type of my actual protein. Specifically, I have a homolog structure, with slightly different start and stop residues, and several non identical a.a.s relative to my
I believe FFAS03 will renumber aa's based on the sequence you plug into it, and then give you two choices - complete replacement of all residues, or just the exact matches and stub to serine for the others. cheers, On Thu, Feb 3, 2011 at 8:11 AM, Justin Hall hallj...@onid.orst.edu wrote: Dear
CHAINSAW retains conserved amino acids but prunes nonconserved residues to the C-beta or C-gamma atom. PDBSET can renumber I think Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campus Cantoblanco E-28049 Madrid, Spain
I believe ccp4 chainsaw will do all three: truncate nonconserved AA (to gly, ala, or all atoms in common), rename residue type, and renumber (if you use clustalw alignment which has residue numbers for query and target). It even renumbers around gaps and insertions in an intelligent way.