Personally, I like the ability to at least have a sanity check of the HETNAM with the dictionary - and if they do not match - do not use it... Assuming people provide a unique name in their dictionary - even if it is FOO1, FOO2, etc - this could catch the issue. This assumes that the refinement programs output such information.
For places that one cannot ensure the dictionary restraint file is proper, maybe a coot preference/configuration of ligands in which coot should not assume the loaded dictionary is correct. One could put LIG, DRG, XXX in it. If someone then manually reads in a restraint file - then you use it. Does coot save the location of dictionary files manually loaded? Ezra Paul Emsley wrote: > Thanks to all contributors, I have been informed, educated and > entertained. > > A bit of background perhaps... (it seems that I have been living in > the 0.7 world long enough to forget that not everyone else is here). > "[T]he viewer programs don't care about the restraint dictionaries" > says Seth Harris - haha - in olden Coots that was the case... :) It > is my hope that Coot will be used for comparison, evaluation, > validation and manipulation of ligands in protein-ligand complexes and > their electron density. > > My current obsession is with chemical structure diagrams - here's a > recent screenshot: > http://lmb.bioch.ox.ac.uk/coot/screenshots/Screenshot-example-2010-01-02.png > > > ... and here's one I made earlier today, illustrating the sorts of > problems I am trying to handle (PI3 Kinase ligand, 4a55): > http://lmb.bioch.ox.ac.uk/coot/screenshots/Screenshot-Coot-prodrg-valence-problem.png > > amusing, eh? > > Anyway, to make the chemical diagram and the 3D bonding representation > I need to construct a description of the ligand that contains bond > orders. Hence restraints. So yes, let me emphasize that this is > mostly for drawing pictures and I don't see the use case of refinement > of multiple different ligand complexes as very useful. > > I do like Dale's idea - the use of HETNAM and synonyms - so, as I > understand it, the PDB file has a residue called LIG and the > dictionary has a comp-id of > "2-(N-methylmethanesulfonamido)-6-(propan-2-yl)pyrimidine" (or > XYZ0123456 or whatever) and a HETNAM record in the PDB file provides > the mapping. Is this a solution? It is attractive because it > requires very little work from me. > > I did consider Judit's idea, i.e. check the atom names in the > coordinates against the dictionary before bonding. I thought that > there may be (too many?) pathological cases where the names did match > (at least for ligand fragments) but the chemistry did not. Let me > know if you think that I need not worry so much about that. This is > relatively easy to do. However, this only solves the "tangle" problem > - and I think that that for practical purposes that may be covered now > as I have recently turned off restraints auto-loading for several > "special" three-letter codes - one can (at least) see "noddy" bonding > instead of a tangle. > > To answer Garib's point: yes, in Coot there is indeed a single > table/dictionary of restraints, with the key/index being the > comp-id/residue-name. It applies to all molecules. I had not before > considered the option of embedding monomer restraints inside a Coot > molecule - that might be a cleaner solution. I will ponder on that. > It does mean that you will have to read restraints after reading > coordinates though. > > And yes, I do occasionally wonder how computational chemistry software > (Maestro, Vida for example?) solves this problem. Presumably such > software is used to show several overlaying ligand structures (all > called "LIG"?). And computational chemists like to see chemistry, and > not just coloured sticks, right? > > Thanks, > > Paul. >
