Not easily. It can be done in case you want to compare the same (or very similar) molecules (e.g. ligands) in two different structures, for example, to compare a ligand before, LEO, and after refinement, TEST, proceed as follows:

  O > s_a_o qa.pdb leo ;;;;;
  O > s_a_o qb.pdb test ;;;;;

now edit the files so that they only contain corresponding atoms; call ALL atoms " CA " and give each atom its own residue number (here: a200, a201, ..., a210). Then:

  O > s_a_i qa.pdb qa
  O > s_a_i qb.pdb qb
  O > lsq_expl
 Lsq > Least squares match by explicit definition of atoms.
 Lsq > Given 2 molecules A, B the transformation rotates B onto A
 Lsq > What is the name of A (the not rotated molecule)? qa
 Lsq > What is the name of B (the rotated molecule)? qb
 Lsq > Now define what atoms in A [=QA] are to be matched to B [=QB]
 Lsq > Define atoms from QA (the not rotated molecule): a200 a210
 Lsq > Define atoms from QB (the rotated molecule): a200
 Lsq > Define atoms from QA (the not rotated molecule):
 Lsq > The 11 atoms have an r.m.s. fit of 0.659
 Lsq >  xyz(1) =     0.9995*x+   -0.0197*y+    0.0249*z+   -0.0576
 Lsq >  xyz(2) =     0.0183*x+    0.9984*y+    0.0535*z+   -2.3668
 Lsq >  xyz(3) =    -0.0260*x+   -0.0530*y+    0.9983*z+    3.0084
 Lsq > The transformation can be stored in O.
 Lsq > A blank is taken to mean do not store anything
 Lsq > The transformation will be stored in .LSQ_RT_qab
  O > db_ki qa_* db_ki qb_*
 Heap>  Deleted QA_ATOM_XYZ
 Heap>  Deleted QA_ATOM_B

Now you can apply the transformation .LSQ_RT_qab to an object or a molecule.