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Generating transformed coordinates using TRANSFORM

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.


next up previous contents
Next: Generating averaged coordinates Up: Worked examples Previous: Protein domain databases   Contents