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Generating REFI Geometry Files from TNT Files

Any conversion of data from one format to another presents problems. The severity of the problems depends upon the amount of difference in the basic structure of the data itself. The reformatting a structure factor file would seem to be simple because everyone agrees to use integral indices and agrees that there are three of them. However even this case is not so simple. Different formats require different asymmetric units, and different sorting. There are other differences like the difference between structure factor intensities and amplitudes.

The conversion of TNT's ideal geometry data files to those of Frodo and O presents a particularly difficult problem. These file formats embody quite different views of the data required to define the conformation of a molecule.

Because of the fundamentally different representation of the data it is impossible to generate a REFI format file in TNT without some intervention on your part. It is almost certain that you will have to add additional GEOMETRY statements to your geometry definition to satisfy this program. In addition you may discover that you need to alter some existing GEOMETRY statements.

The up side of this is that you might very well uncover errors of ommission in you TNT geometry definition. TNT does not provide any assurance that the ideal geometry definition you supply is complete. In fact, it is a useful feature of TNT that you can leave out restraints for particular geometry items if you are really unsure what their value should be. The REFI format does not allow any of its values to be left undefined. If you neglected to define a particular bond angle no program in TNT will inform you of the problem. The conversion to REFI format will.

Dale Edwin Tronrud
Thu Jul 6 23:24:57 PDT 2000