Transformations, which may or may not be included in the domain
definition given above are in the sense:
Xnew | R11 R12 R13 | Xold V1 Ynew = | R21 R22 R23 | Yold + V2 Ynew | R31 R32 R33 | Zold V3
Xnew = (R11*Xold + R12*Yold + R13*Zold) + V1 Ynew = (R21*Xold + R22*Yold + R23*Zold) + V2 Znew = (R31*Xold + R32*Yold + R33*Zold) + V3
If initial transformations are obtained in some other way (eg.
those taken from a PDB file) they may be passed to STAMP if they
are in the above format. As far as I can make out, this is the
standard used in the PDB, but one can never be sure.
If no transformation is given, then the domain is assigned a unity rotation matrix and zero translation vector.