Use the following procedure to create a database to be used by the Search Fragment Database utility.
1. From the Brookhaven database, select a set of protein coordinates files that have good resolution and include different structure types.
2. Construct a file (dmlist) that contains a list of these protein coordinate files. Use the following format in constructing the file:
3. Run the program $HYD_MSF/dmprep. The program prompts for the name of the file (dmlist) containing the list of proteins and asks for a name for the distance matrix file (dmfile.new) to be created. The program then reads each protein coordinate file and constructs a distance matrix file. It also creates a QUANTA input command file. The command file is used from within QUANTA to generate an MSF for each of the protein coordinate files. You are prompted to name this file.
The dmprep executable distributed with QUANTA can handle up to 2,000 proteins with limits of 2,000 residues and 100,000 Ca distances per protein. The FORTRAN sources for dmprep (dmprep.f and dmsubs.f) are also distributed. This gives you flexibility to increase the dimensions as you need them.
4. Move the distance matrix file to the $QNT_ROOT/dmatrix directory and rename it to dmfile. Because the variable $HYD_DMF is already defined in the QUANTA environment as $QNT_ROOT/dmatrix/dmfile, you can do this easily by typing:
cp dmfile.new $HYD_DMF
where dmfile.new is the filename of the distance matrix file created in step 3.
5. To create required MSFs, start QUANTA and type @command_file, where command_file is the name given to the QUANTA command file. Respond appropriately to the dialog boxes. Treat the sixth character in the atom field as a disorder using the no-hydrogen dictionary file, and exclude symmetry in the molecular structure file.
6. Move the newly created MSFs to the directory $MSF_LIB.