-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 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 GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.15 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFScPxSUxlJ7aRr7hoRAi1TAKDrjtWhH5sCw/3kwPimT/0WVE4oWwCgovPM 4bWow+/SfAp46XnoxD5UJXE= =YXln -----END PGP SIGNATURE-----
