On 7-5-2006 13:21, Bob Hanson wrote:
Interesting. I like the way it can all be done with integers. OK, now I
have it set that it IS identifying all true molecules, and in principle
it COULD be saving some information about which atoms were produced by
which symmetry operation. Problem is, doesn't it matter which order you
apply these (redundant) symmetry operations? How does that work? What's
the convention? Or would it be enough to be able to select
"symmetry-derived sets" without the assumption of order? - that is, I
guess it would just use the order presented in the file. BUT then I need
to know in exactly what order to apply LATT to SYMM. Right? Because I
basically have two loops: "loop through the symmetry operations" and
"for each symmetry operation, loop through the LATT
translations/inversions." So is there some precise order that is
dictated by convention here?
In a CIF all of the symmetry operations are explicitly represented, so,
the number of each operation runs from 1 (identity, i.e., x,y,z) though
n for the space group (including all lattice transformations). It is
only in SHELX or, possibly PDB, where only the irreducible set of
symmetry operations are presented and the lattice transformations are
deduced. So you could take the SHELX format and simply create the
equivalent of a CIF-style list:
-- set the x,y,z operation to #1
-- add the operations from the SHELX file
-- take each of the above and add the lattice transformations to form
additional operators
This should now give identical lists of symmetry operators (including
order) for the CIF-based files and the SHELX-based files.
Now you only have one loop: for all symmetry operators loop over all
atoms (or vice versa depending on your preferred programing
style/efficiency).
Also, does 3555 refer to a molecule in the chemical sense, or a set of
"primitive atoms"?
It depends on if you have invoked the "connect all atoms into smallest
group on file load" option or not. Let's assume the atoms come in as a
connected molecule for now and say "primitive atoms".
Rich
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