Re: [modeller_usage] Check_a_337E> Structure not read in

[Modeller Caretaker <>]

David Mathog wrote:
> First time trying to use Modeller and the log file terminates
> with:
>
> check_a_337E> Structure not read in.

There is usually a warning before this with more information. Usually 
it's because your alignment sequence doesn't match the PDB ATOM and/or 
HETATM records (Modeller does not read SEQRES).

> Modeller seems to have read the alignment alright, although this bit:
>
>   (def)remove_gaps=True
>
> is a little worrisome, since there are a couple of gaps in the
> alignment.

That doesn't remove all gaps, of course - only gaps which are present in 
every sequence (which would be redundant, of course). See
http://salilab.org/modeller/manual/node177.html

It sounds like your PDB has missing residues, in which case these 
residues would need to be removed from your alignment. See 
http://salilab.org/modeller/wiki/Missing_residues for an example.

	Ben Webb, Modeller Caretaker
--
             http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage