I was trying to generate the second monomer of a homo-symmetric
dimer from an x-ray crystallographic monomer deposited with a, b, c, alpha,
betta and gamma unit cell constants. The resulted dimer using your sample
protocol on page 268-269 (with proper unit cell paramerters and rotation
operation) is correct in terms of overall orientation that two monomers
relate to each other, but with one little problem. The some atoms of the
residues on the very far tips of the two monomer structures are screwed up
and their coordinates on Z-axis are not correct. The Z-axis coordinates of
these atoms on monomer I&II are exchanged. In another words, for example,
these atoms on monomer I have correct monomer I's x- and y-axis and monomer
II's z-axis coordinates! The interpretation of this is that these atomes
are physically located outside of unit cell. I am wondering if xplor
program can handle this type of the problem within itself.
I am looking foward to hearing from you soon on this matter.