CorrectingMisalignmentOfPDB

In the following example we look for a symmetry axis of a PDB file and correct it in the PDB. The search for the symmetry is performed using the Xmipp program FindCenter3D which only works with voxels

$ xmipp_phantom_transform -i mypdbfile.pdb -o mycenteredpdbfile.pdb -pdb -center_pdb
$ xmipp_convert_pdb2vol -i mycenteredpdbfile.pdb
$ xmipp_findcenter3D -i mycenteredpdbfile.pdb -rot 0 360 5 -tilt 0 2 0.1 -rot_sym 7

The best axis provided by findcenter3D is rot=270 and tilt=1.6

$ xmipp_phantom_transform -i mypdbfile.pdb -o mycorrectedpdbfile.pdb -pdb -center_pdb -euler 270 1.6 0

-- Main.CoSS - 10 Aug 2007