How can I adjust a molecule or fragment to have ideal coordinates?
This assumes you’ve got some known coordinates for, say, a solvent molecule and you want to tidy up a molecule in your structure because it isn’t refining very well. We find a nice orthoxylene molecule (eg. CSD entry WAFKOD) and we want to correct our rather poor orthoxylene molecule which is numbered C101-C108 starting on one methyl and ending on the other, going the long-way around the ring. That atoms we want to correct are specified on the TARGET directive. The coordinates of atoms of the ideal molecule are given on ATOM directives, following a SYSTEM directive with the cell parameters of the structure that the ideal molecule is taken from.
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