REFORIGIN (CCP4: Unsupported Program)

NAME

reforigin - apply best origin shift to PDB atom co-ords according to reference file

SYNOPSIS

reforigin XYZIN working.pdb XYZREF reference.pdb XYZOUT output.pdb [ SPACEGROUP <sg_name or sg_num> ] [ DMAX <dmax> ] [ CAONLY <true | false> ]

DESCRIPTION

"reforigin" automatically re-origins (and changes the a.u. if necessary) a PDB dataset to a reference dataset (useful after MR when the model and target structures have the same space group and cell, or nearly the same cell). The required transformations are point-group dependent.

INPUT AND OUTPUT FILES

The following input and output files are used by the program:

Input Files:

XYZIN
Input PDB file which is to be re-origined.
XYZREF
Input PDB file with reference structure.
The two files XYZIN and XYZREF need to contain the same list of atoms.

Output Files:

XYZOUT
Output file that contains the coordinates after the transformation and origin shift.

OTHER INPUT

Note that this input is currently set on the command line.
SPACEGROUP <sg_name or sg_num>
This is optional if the spacegroup is in the working CRYST1 record.
DMAX <dmax>
Maximum RMS deviation for fitting co-ordinates: default = 5 A.
CAONLY <true | false>
If true, use only the CA atoms to determine required transformations. If alternative conformations are present, the "A" conformation is assumed. The default is false, i.e. use all atoms.

OUTPUT

If the program is able to fit XYZIN to XYZREF, it will output: 


Translation modulus:                  3        3        6
Equivalent position:                        -X+Y,  -X,  Z
Fractional origin shift:         0.6667   0.3333   0.3333
Orthogonal origin shift:         28.997   16.741   52.138
RMS deviation:                    3.428
This gives the primitive symmetry operation applied (e.g. -X+Y, -X, Z) and the translation (centering and/or origin shift, e.g. 2/3, 1/3, 1/3). The RMS deviation is between the atoms of XYZREF and the transformed atoms of XYZIN.

PROBLEMS

The program assumes the standard orthogonalisation convention.

SEE ALSO

pdbset - can apply arbitrary translations, see SHIFT keyword.

AUTHORS

Ian Tickle, Astex Technology