OK, this code is checked in as part of 11.1.29. I have bit more
testing to do on that today, and then that should be available. The
flag looks like this:
version=11.1.29
# adds applySymmetryToBonds (default: FALSE)
# 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 Hanson
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