UNMTRIX(1)

NAME

unmtrix - expand MTRIX records in PDB files

SYNOPSIS

unmtrix [-i original_PDB_file] [-o new_PDB_file] [-m

MTRIX_serial_id]

DESCRIPTION

Unmtrix reads a Protein Data Bank file and generates coordinates for subunits specified by MTRIX records. The -i argument specifies the input PDB file. If no input file is given, unmtrix will read from standard input. The -o argument specified the output PDB file. If no output file is given, unmtrix will write to standard output. Normally, unmtrix will generate coordinates for all MTRIX records which do not have atoms associated with them. When given the -m argument, unmtrix will generate coordinates only for the MTRIX records that match the given MTRIX_serial_id.

EXAMPLES

Since MTRIX records contain a 3x3 rotation matrix as well as a 3x1 translation vector, the records are always given in groups of three, like this:

     MTRIX1   1 -0.725530  0.071920 -0.684420       68.86822    1
     1RSL 138
     MTRIX2   1 -0.000100 -0.994540 -0.104400       81.59939    1
     1RSL 139
     MTRIX3   1 -0.688190 -0.075680  0.721570       32.52771    1
     1RSL 140

The second column is a serial number for the three-record group. If additional MTRIX records were necessary for additional subunits, each triplet would have a unique serial number. The third through fifth columns contain the rotation matrix. The sixth column is the translation vector. The seventh column indicates whether the coordinates generatable with these records are already present in the PDB file. If there is a ``1'' in the seventh column, the coordinates are present in the entry. If the column is blank, the coordinates are absent. The trailing columns are record serial number information, found on all PDB records.

The above MTRIX records would be for a subunit whose coordinates are already present in the PDB entry, indicated by the ``1'' in the seventh column. Unmtrix will always ignore such records. Unmtrix will only operate on MTRIX records with a blank seventh column, an example set of which is shown below.

     MTRIX1   1   -.91000   -.41511    .00700        -.29750

     1REI 128
     MTRIX2   1   -.41396    .91000    .02598        -.29878
     1REI 129
     MTRIX3   1   -.01700    .02136  -1.00000       33.14600
     1REI 130

SEE ALSO

Protein Data Bank, Atomic Coordinate and Bibliographic Entry Format Description.

AUTHOR

Conrad Huang

Computer Graphics Laboratory

University of California, San Francisco