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Dear Andreas,

I am not sure there is a convention, but there has been a decision.
When you deposit a structure with the PDB, they place all ligands
including water molecules to the respective nearest macromolecular
chain. I found this rather annoying the other day as I looked at the
polymerase structure and wanted to take a look at the Zn-atoms.
Instead of navigating through chain Z, where probably many
crystallographers would have put them, I had to check the PDB (text)
file for the correct chain and residue number and enter this into the
'goto'-field of coot.

If I understand some people correctly, this is not a shortcoming of
the PDB-format, but of the software developer developing the software
I used. So I am waiting for the next version of coot/mmdb with voice
recognition where I can just say "Coot, please centre on the next Zn
in this structure". Or at least opening a pop-up window saying "This
is you coot speaking. This structure contains 6 Zn atoms, and I feel
that you are interested in looking at their environment. Please click
'yes' to centre on the next Zn-atom I think is most suitable for you
to look at" ;-)

Best,
Tim

On 10/30/2013 01:09 PM, 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
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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