The program TRANSFORM can be used with any STAMP alignment file containing domain
descriptions to output a set of PDB format files for display or
further analysis. For example, running:
transform -f globin.5
should write the following to the standard output:
TRANSFORM R.B. Russell, 1995 Using PDB files Files will not include heteroatoms Files will not include waters Domain 1, 1lh1 => to 1lh1.pdb Domain 2, 2lhb => to 2lhb.pdb Domain 3, 1ecd => to 1ecd.pdb Domain 4, 4mbn => to 4mbn.pdb Domain 5, 2hhbb => to 2hhbb.pdb Domain 6, 2hhba => to 2hhba.pdb
A set of PDB format files containing the superimposed
coordinates is generated. Running the program as shown above will produce one PDB
file for each domain identifier. If one wishes to look at the
superimposed structures together (in the same file), then the
option -g (i.e. graphics) can be used:
transform -f globin.5 -g -o globins.pdb
which should output the following:
TRANSFORM R.B. Russell, 1995 Using PDB files Files will not include heteroatoms Files will not include waters All coordinates will be in file globins.pdb Domain 1, 1lh1 => to globins.pdb (chain A) Domain 2, 2lhb => to globins.pdb (chain B) Domain 3, 1ecd => to globins.pdb (chain C) Domain 4, 4mbn => to globins.pdb (chain D) Domain 5, 2hhbb => to globins.pdb (chain E) Domain 6, 2hhba => to globins.pdb (chain F)
This options puts transformed coordinates for each domain into one file
(specified by -o, in this example it is `globins.pdb'). Each domain will
be labelled sequentially with a different chain identifier (i.e. A, B, C,
etc.). Note that only `globins.pdb' is included in the example directory.
By default, TRANSFORM does not include heteroatoms in the output. If you
wish heteroatoms to be included, then add the -het option to the transform command.
If you wish waters to be included in the file add the -hoh option.
Note that heteroatoms/waters are sometimes included that fall outside the
range of your domain descriptor. This may seem silly, but it
is difficult to determine which heteroatoms are associated with which residues
given PDB format.