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From: Robert H. <ha...@st...> - 2013-08-20 23:19:10
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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 > > > > > > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- 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 |