There is a useful, but out-of-date program in the CCP4 suite called
watertidy.
it analyses the H2Os and after applying symmetry to move them close to
the protein, relabels them according to the protein atom they are closest to
So for protein chain A you can output a water chain W where the
W"residue" number is the same as the protein residue in chain A, and
there is a code flagging which atom in the A residue is h-bonded to the
water
so for A ALA 1 the water associated with N ALA 1 A would be labelled
O00 HOH 1 W
O
ALA 1 A would be labelled O01 HOH 1 W
etc.
It is very useful when you want to find HOHs which are equivlent in
models with several homologous protein chains in the asymmetric unit.
However the naming of HOH atoms as O00 O01 etc breaks the PDB definition
and many downstream programs fall over..
Does anyone have a better idea for a replacement tool?
Eleanor
