New restraints, same name

From: Ingo P. Korndoerfer
Date: 25 January 2012 08:15

... 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.
>

----------
From: Garib N Murshudov

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