Dear all,
this water discussion is flowing increasingly towards a place where I
feel a bit out of my depth.
What is the convention for numbering water molecules? Is there
preference for:
- putting waters into a separate chain (W for water or S for solvent)?
- splitting waters according to the peptide chains in the structure?
- appending all waters to chain A?
Thanks.
Andreas
On 30/10/2013 11:57, MARTYN SYMMONS wrote:
At deposition the PDB runs a script that renumbers authors' waters
according to a scheme based on the residue they are nearest from N to C
terminus along each chain. This renumbering started when waters were
assigned to macromolecular chains rather than getting a chain id of
their own. I have failed to find the rationale explained in any PDB
documents - but it could be motivated by this sort of consideration when
waters from different chains or entries are to be compared. Having said
that I do not know if there are any cases where this approach has
successfully matched waters. ..
However an associated step which is certainly a help is that, in the
case of multiple chains, the crystal symmetry is applied to replace
waters with their symmetry equivalent position if it is closer to a
different chain.
I believe a freely available program implementing a similar approach is
WATERTIDY in CCP4 which might be a good place to start. It gives a
pretty complete output, detailing residues actually H-bonded to the
waters, and you could parse that for further analysis and comparisons.
Best wishes.
Martyn
--
Andreas Förster
Crystallization and Xray Facility Manager
Centre for Structural Biology
Imperial College London
