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

[Modeller Caretaker <modeller-care@ucsf.edu>]

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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