> # applySymmetryToBonds
> #
> # When set TRUE, this flag instructs Jmol when applying symmetry
> # to atoms, as in "load xxx.cif {1 1 1}", to also apply symmetry
> # to the bonds indicated in the file. The flag is useful when
> # normal Jmol autobonding would not properly connect atoms, but
> # the model is "molecular" -- the base atom coordinates are correct
> # for whole molecules. The flag should NOT be used in cases where
> # the application of symmetry operations creates new bonds that
> # were not present in the original set, as for quartz.cif, where
> # there is only one bond initially, and after applying symmetry
> # new bonds are created that are between atoms that were created
> # using two different symmetry operations.
>
> This appears to work perfectly for the example file Aiden provided.
> It does connect the atoms properly in quartz.cif, but some bonds
> are missing, as
> noted above. It also fails to connect bonds properly in a test sample
> I have that involves a cif file with alternative locations but bonding
> only shown for one alternative. So there are definitely limitations,
> and I have set the default to be FALSE -- no change from previous
> behavior. You must explicitly include:
>
> applySymmetryToBonds = true
>
> prior to loading a file to instruct Jmol to carry out this bonding
> algorithm.
Bob, you are a pearl. Thanks heaps. I look forward to testing this out.
Cheers
Aidan
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