I'd like to support that. Feature request...
On Wed, Aug 21, 2013 at 12:29 PM, Tom Daff <[email protected]> wrote:
> Thanks for the quick reply!
>
> > 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.
>
> This is working great, thanks! I think there are a couple more ccdc bond
> types that are defined for MIF files in the International Tables G which is
> also copied out here:
>
>
> http://cima.chem.usyd.edu.au:8080/cif/skunkworks/html/ddl1/mif/bond.html#_bo
> nd_type_ccdc
>
>
>
> > 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.
>
> I work with 3d periodic structures, for which I have all the bonding
> explicitly specified in the cif. Specifically, what I hope to see is that
> when I do `load "MIL-47.cif {2 2 2} `, it is the {2 2 2} representation
> with
> the unit cell intact and with the bonding that has been defined in the
> GEOM_BOND section. From my testing it seems that either the GEOM_BOND gets
> used and there is no way to stop the unit cell being thrown out (without
> the
> {2 2 2} or using filter = "molecular"); or using the unit cell causes the
> autobonding routine to ignore the GEOM_BOND and connect only with distance
> checks (autobond OFF results in no bonds). In most cases this is probably
> fine, but since it is now possible to specify bond types, and I have some
> close atoms that are not supposed to bond, it would be nice to be able to
> force both GEOM_BOND and unit cell on.
>
> Mostly I was curious as to whether I had missed an option somewhere that
> enabled this. Having worked a bit with cifs I understand that supporting
> everybody's particular use case is not always an option, but I thank you
> for
> following up on this.
>
> 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
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