That is the plan and hopefully with help of people from pdb coot, buster, phenix, refmac, ccp4 programs will all use mmcif with ligand descriptions inside. Good will is there, a little bit work is needed.
Regards Garib On 25 Jan 2012, at 08:15, Ingo P. Korndoerfer wrote: > ... and why don't we move on from pdb format to something a bit more > modern ? > > i think it would only require a handful of programmers to agree on this > and the rest would (have to) follow. > > i.e. if coot and refmac could both read and write something more modern > we'd have a huge part of ccp4 world > covered. > > are we thinking of ourselves at working at the frontiers of science or > not ... (... o.k. ... different topic, but you get the idea ...) > > ingo > > On 25.01.2012 03:53, 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. >> Garib N Murshudov Structural Studies Division MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH UK Email: ga...@mrc-lmb.cam.ac.uk Web http://www.mrc-lmb.cam.ac.uk
