The LoopFinder uses a database for extraction of essential PDB information
regarding the loops. To give LoopFinder some speed, this database holds a
small degree of organisation. The first step in this otganisation
is that the database is split into three similar parts that are stored in the
directories data2, data3, and data4. These three directories hold all data
needed for searches with an anchor-length of 2, 3, and 4 Cα atoms,
Content per loop
For each loop (with length ranging from 5-26 amino acids) the database holds
The length of the loop
The PDB chain identifier (of all residues in the loop)
The number of the first residue in the loop
The 4-character identifier of the PDB file where the loop comes from
The character H or L that indicates whether this file is part of the
high quality subset of PDB files (H), or not (L).
The X,Y,Z coordinates of 8 Cα atoms.
The coordinates mentioned at the last bullet point are those of the
first and last 2, 3, or 4 residues of the loop.
The coordinates are stored for 8 Cα atoms; also if the user only wants
2, or 3 anchor residues. In these two cases the last 4, respectively 2 sets
of X,Y,Z coordinates are just meaningless random numbers that are not being
used by the LoopFinder.
Database file names
In each of the three directories (data2, data3, data4) you find files with
names like fort.110, fort.111, etcetera. The numnerical part of these file
names are two times the distance between the first and the last Cα in
the loop, rounded to the nearest whole number. Given that it seems highly
unlikely that anybody will ever search for all loops that match with an
allowed error greater that 1.0 Ångstrom, this allows LoopFinder to
stop searching after 3 of the 25 database files have been scanned.
Database file format
FORTRAN works much faster with unformatted (only computer readable) files
than with formatted (also human readable files). The database therefore
consists of unformatted files.
To help programmers work with these files we added the very small
FORTRAN program ReadOne.f that reads the smalles
database file (data2/fort.105) and prints its contents. You execute and run
this program in the main area where you keep all your LoopFinder files with