MOLSCRIPT question...help!

[Dirk Bussiere]

I am once again using that annoying program MOLSCRIPT to make a few
figures and, as usual, I am running into problems.  I am using it to
make a figure 
of a protein:DNA complex with the protein and DNA read in as seperate
files.
I got the view I wanted on O, generated the transform matrix and read
it from
the o_plot file, did the usual 'transform atom *' and the matrix.  The
protein is positioned properly in the output (i.e. is equivalent to the
O
view), but apparently the DNA was not aligned by the 'transform'
(either that
or it was aligned incorrectly by it).  Has anyone run into this
problem, and
if so, how do I correct it?? Thanks!