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This program takes a transformation file, either from ALIGNFIT, STAMP, or SORTRANS and outputs a series of PDB format files containing the specified coordinates transformed as specified in the given file.

The format is:

transform -f <transformation file> [ -g -het -hoh -o <output file> ]


`-het' Include hetero atoms. Hetero atoms are normally not included in the output.
`-hoh' Include waters.

`-g' Graphics output. This mode puts all transformed coordinates into a single PDB file, and labels the chains for domains sequentially (after their order in the transformation file) with A, B, C.. etc. This allows fast analysis of the structures graphically (i.e. using Rasmol) since one need only colour each chain a different colour to see the superimposition. The default file for writing the coordinates using this mode is `all.pdb', but this can be changed (see below).

`-o <output file>' When using `-g', this option allows the specification of a file to contain the transformed coordinates. The default is `all.pdb'

The PDB files will be named <identifier>.pdb (except when running using the `-g' option).

Geoff Barton