Check_a_337E> Structure not read in
First time trying to use Modeller and the log file terminates with:
check_a_337E> Structure not read in.
There's nothing wrong with the PDB file as far as I can tell, several other programs will read it.
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. In fact, that's the whole point, I want to see if modeller can close the gaps so that I don't have to do it manually in a modelling program. The gaps are part of the structure that flaps around in solution so it isn't in the PDB file, but it has to be added before Gromacs will accept the structure.
Thanks,
David Mathog mathog@caltech.edu Manager, Sequence Analysis Facility, Biology Division, Caltech
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
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David Mathog -
Modeller Caretaker