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