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> ]
options:
`-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).