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Re: CIF dicsussion on chemical structure

  • To: corecifchem@iucr.org
  • Subject: Re: CIF dicsussion on chemical structure
  • From: Peter Murray-Rust <pm286@cam.ac.uk>
  • Date: Thu, 14 Oct 2004 20:28:13 +0100
  • Cc: smt40@cam.ac.uk
I had an extremely good visit to Chester and many thanks to PeterS BrianMcM 
and others. In summary I ran CIFSAXDOM and CIF2CML over this months ActaE 
CIFs and found very good conversions to chemistry. Even with disorder 
(which had worried me) the author/editor curation was good. By taking 
_atom_site_disorder_group="." or ="1" all structures gave reasonable formulae.

The main problems are:
- symmetry. We are going to test whether using the additional bonds, angles 
and torsions we can normally generate the symmetry related atoms
- disorder. we have to assume the connectivity of disorder groups is 
constant or that the first one is definitive
- charges. Almost all structures had formal charges in the formulae and we 
shall test this out.
- hydrogens. We did not see any missing hydrogens

We have not yet mapped formulae onto disjoint moieties.

With this level of quality it should be possible to define good protocols 
for many systems. I am on the road shortly but hope to find time to create 
some exemplars.

I note that the _atom_site_disorder_* fields are not crystallographic but 
chemical annotations (by and large they do not affect the interpretation of 
the diffraction experiment unless they are used for librational analysis. 
Is that fair? If so, I would propose that we use other fields in _atom_site 
for chemical annotation.

here is the first question we have to answer:
- what information is given by the diffraction and its analysis; and what 
by the chemistry given from elsewhere?

We can envisage:
- elementTypes unknown chemically but modelled to fit the diffraction
- elementTypes known chemically but unused in the diffraction model (e.g. 
trace elements or very light ones)
- spin states known chemically but undetected in diffraction.
- (possibly) fluxional behaviour which affects the chemical description of 
the molecule. The chemist may value a dynamic description rather than the 
fixed positions returned by crystallography.

To accomplish this I this is valuable to be able to create additional 
annotation in the _atom_site table and to have atoms in there which do not, 
or cannot contribute to the diffraction (i.e. occupancy = 0.0) Does this 
look reasonable?

In haste


Peter Murray-Rust
Unilever Centre for Molecular Informatics
Chemistry Department, Cambridge University
Lensfield Road, CAMBRIDGE, CB2 1EW, UK
Tel: +44-1223-763069

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