Thanks to all who contributed to the discussion on solving the problem
with the COMPARE scripts. I deleted the extra chains, etc from the xray
PDB and then renumbered the residues so that they matched with the MODEL
pdb. This solved the problem when comparing the model and the actual
structures. But when I tried to add the template to the comparison (just
like they do in the example script) along with reading in the alignment
file, MODELLER complains. The error seems to be with the MODEL and xray
pdb, not the template... that seems weird since it was successful without
the template or the alignment file. I'll look into it some more.
Again thanks for the responses.
Troy Wymore