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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.