REFORIGIN (CCP4: Unsupported Program)
NAME
reforigin - apply best origin shift to PDB atom co-ords according to reference fileSYNOPSIS
reforigin XYZIN working.pdb XYZREF reference.pdb XYZOUT output.pdb [ SPACEGROUP <sg_name or sg_num> ] [ DMAX <dmax> ]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.
Output Files:
- XYZOUT
- Output file that contains the coordinates after the 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.
PROBLEMS
The program assumes the standard orthogonalisation convention.SEE ALSO
pdbset - can apply arbitrary translations, see SHIFT keyword.