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.)