In PDB format files, each polymer is assigned a unique chain ID. Chain
IDs for all bound moieties and waters are assigned based on their
proximity (number of contacts) to the nearest polymer. Once the polymers
and non-polymer residues associated with them are assigned chain IDs,
they are also assigned unique residue numbering with the order polymer
residues, ligands and then waters.
Please see: http://www.wwpdb.org/procedure.html#toc_4
The wwPDB has established this rule to improve the usability and
interpretation of the structural data. Assigning the same chain ID for
all moieties associated with a polymer enables rapid and uniform
identification of feature analysis.
Sincerely,
Rachel Green
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Rachel Kramer Green, Ph.D.
RCSB PDB
kra...@rcsb.rutgers.edu
Twitter: https://twitter.com/#!/buildmodels
Facebook: http://www.facebook.com/RCSBPDB
On 10/30/2013 8:09 AM, Eugene Krissinel wrote:
This is to be answered by PDB people, who definitely read BB :)
Would be nice to have a tool common between CCP4/Phenix and the PDB which sorts
this out
Eugene
On 30 Oct 2013, at 12:09, Andreas Förster wrote:
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
