REFORIGIN (CCP4: Unsupported Program)
- apply best origin shift to PDB atom co-ords according to reference file
reforigin XYZIN working.pdb
[ SPACEGROUP <sg_name or sg_num> ]
[ DMAX <dmax> ]
[ CAONLY <true | false> ]
"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:
The two files XYZIN and XYZREF need to contain the same list of atoms.
Input PDB file which is to be re-origined.
Input PDB file with reference structure.
Output file that contains the coordinates after the transformation and origin shift.
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.
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.
The program assumes the standard orthogonalisation convention.
pdbset - can apply arbitrary translations,
see SHIFT keyword.
Ian Tickle, Astex Technology