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Re: [modeller_usage] Multi-chain/multi-template Modeling



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
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