Re: [Jmol-users] Bonding in cif files

[Robert H. <ha...@st...>]

Easy question first: _ccdc_geom_bond_type  should not be a big problem. I
do see what you are talking about. For example:

http://www.rsc.org/suppdata/cc/c2/c2cc34714h/c2cc34714h.txt

has "A" for aromatic. That is no problem.


A preliminary attempt is at

http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.4_2013.08.20c.zip

But, like others, that's for the default loading, not for a set of unit
cells.

Harder question: unit cell vs molecular. Right now there is a filter
"MOLECULAR" that basically means "Just give me a molecule, not a full unit
cell." It's like loading a model from any other format, but here from a CIF
file.

Tell me again what exactly you would like to see? Is it full bonding with
any number of unit cells? Might be able to do that; have to think about it.

Jmol appropriately or not handles bonding in CIF with some wariness. The
overall idea is that if bonding is present, that might represent molecular
structures, and we want a default load for that to be simply a molecule,
not a unit cell showing odd fragments of molecule. It is a rather complex
algorithm. Although we do not read the _geom_bond_site_symmetry fields, we
do read these:

      _geom_bond_atom_site_label_1
      _geom_bond_atom_site_label_2
      _geom_bond_distance

Provided those are there, Jmol will "honor" them and do the bonding. Here
are my notes regarding the algorithm:

   * (1) If GEOM_BOND records are present, we (a) use them to generate
bonds (b)
   * add H atoms to bonds if necessary, and (c) turn off autoBonding
("hasBonds")
   * (2) If MOLECULAR, then we (a) use {1 1 1} if lattice is not defined
(b) use
   * atomSetCollection.bonds[] to construct a preliminary molecule and
connect
   * as we go (c) check symmetry for connections to molecule in any one of
the
   * 26 (3x3) adjacent cells (d) move those atoms and their connected
branch set
   * (e) iterate as necessary to get all atoms desired (f) delete unselected
   * atoms (g) set all coordinates as Cartesians (h) remove all unit cell
   * information.




On Tue, Aug 20, 2013 at 3:05 PM, Tom Daff <td...@uo...> wrote:

> Hi,
>
> I have two questions regarding the reading of bonding in cif files.
>
> I would like to load a cif file and use both the unit cell information and
> the bonding information from the GEOM_BOND, but I have tried several
> combinations of options, and can only seem to get the autobonding when the
> unit cell is used. Is there a simple way to achieve this?
>
> Secondly, are there any plans to support reading the bond orders from cif
> files? For example Materials Studio writes the bond orders into a field
> '_ccdc_geom_bond_type' with 'S', 'D', 'T' etc., although I realise these
> are
> conventions and not strict cif fields.
>
> Thanks,
>
> Tom
>
>
>
>
>
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-- 
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900