Re: [modeller_usage] mismatch in the alignment

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

On 9/24/12 2:05 PM, Sajeewa Pemasinghe wrote:
> I am working on the 1qg8 example given at
> http://salilab.org/modeller/wiki/Missing%20residues. I am trying to read
> the HETATM records and the waters.

Generally speaking it is not worth trying to model waters, unless they 
are clearly involved in some interaction with the protein (e.g. in a 
binding site).

> read_te_290E> Number of residues in the alignment and  pdb files are
> different:      661      637
>                For alignment entry:        1  1qg8
>                                   x  (mismatch at alignment position    638)
>   Alignment   wwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwwww
>         PDB   wwwwwwwwwwwwwwwwwwww
>       Match   ********************

Looks like you have miscounted the waters in your PDB file, because your 
alignment has more waters than the PDB does.

	Ben Webb, Modeller Caretaker
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