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
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