On 9/8/17 1:17 PM, Ryan Ehrlich wrote: > I appreciate the input I received from my previous questions, but have > run into something I need more clarification on. I'm attempting to > product models using multiple templates and multiple chains. I'll detail > my steps below:
Your steps look fine to me, including the use of gaps for the single-chain structures. But your 2pye template doesn't look right to me - normally you'd want all the chain breaks to line up, but it looks like your A chain finishes about 15 residues earlier than in the other templates. You probably want to pad this out with gap characters (-) as right now part of your 2pyeB chain is aligned with the A chain of the other templates.
> _modeller.ModellerError: rdpdb___303E> No atoms were read from the > specified input PDB file, since the starting residue number and/or chain > id in MODEL_SEGMENT > (or the alignment file header) was not found; requested starting > position: residue number " 1", chain " A"; atom file name: 2bnu.pdb
This seems pretty self-explanatory, no? In your alignment file you ask Modeller to read ATOM records from 2bnu.pdb, starting at residue 1 in chain A and ending at residue 252 in chain B. But there isn't an ATOM record for residue 1 (it starts at residue 2). (There also isn't a residue 252 in chain B.)
Ben Webb, Modeller Caretaker