The program PDBC may be used to output a set of STAMP readable domain descriptions. Given a list of four letter brookhaven codes and an optional set of chains. This will only work if you have a suitable `pdb.directories' file. See the chapter on installation for details on how to do this.
pdbc -d 2hhba >! globin_fold.domains pdbc -d 2hhbb >> globin_fold.domains pdbc -d 4mbn >> globin_fold.domains pdbc -d 1lh1 >> globin_fold.domains pdbc -d 1cola >> globin_fold.domains pdbc -d 1cpca >> globin_fold.domains
will produce the following output (ignoring comments, which are specified by a `%` in column 0):
/(PDB PATH)/pdb2hhb.ent 2hhba { CHAIN A } /(PDB PATH)/pdb2hhb.ent 2hhbb { CHAIN B } /(PDB PATH)/pdb4mbn.ent 4mbn { ALL } /(PDB PATH)/pdb1lh1.ent 1lh1 { ALL } /(PDB PATH)/pdb1col.ent 1cola { CHAIN A }
Where (PDB PATH) denotes the location of the relevant PDB file on your
system. Note that your PDB files may be called (code).pdb instead, or
may follow some other convention. This is OK, see Chapter 5 (installation) for
details as to setting this up.
Note that there doesn't need to be a filename in the domain file. One
can merely leave it as `Unknown` or some other string (i.e. not empty
spaces), and the programs will try and find where the file corresonding
to the four letter code is one your system. In other words, the files
given in this distribution should work on your system, provided that
you have all the PDB files.
Note that PDBC can be used to probe information about a PDB entry by
using the `-q' option. Try it and see. This is a good test of whether
STAMP has been set up properly on your system. If you just want to test
where STAMP is looking for PDB and DSSP files, then use the `-m' (minimal)
options. This just reports PDB/DSSP files if found and exits.
STAMP database comparisons are computationally intensive, so it is prudent
to avoid comparisons that are redundant (e.g. multiple mutants or binding studies
of the same protein, T4 lysozyme for example).
The STAMP distribution
contains a series of non-redundant databases derived by a parsing of the
SCOP database. These are located in the `STAMPDIR' directory. The files are
derived from SCOP release 1.75. The files were created using the scop2stamp
program, which can be found in the `bin/' directory of the STAMP installation.
Running `scop2stamp' without arguments will list the options that this program accepts.
Domain database | N | Description |
scop.dom | 109747 | All PDB domains classified in SCOP |
scop_species.dom | 13816 | One representative per species of each SCOP protein. |
scop_prot.dom | 9621 | One representative of each SCOP protein |
scop_fam.dom | 3883 | One representative of each SCOP family |
scop_supf.dom | 1950 | One representative of each SCOP superfamily |
scop_fold.dom | 1190 | One representative of each SCOP fold |