It worked good. Then I added DISU as I learned from the manual by
redefining the special_patches(). (Script as below) The new model is
the same as the old one. I don't see disulfide bond between the two
cysteins.
Can any one explain it a bit? Thank you!
Your script looks fine to me. As for why you're not seeing the disulfide
bond, this could have two explanations:
1. Modeller does not add any connectivity information to the generated
PDB file. So your PDB viewer will not "know" to draw a disulfide bond.
Some viewers will just try to guess if such a bond exists by looking at
the distances between residues.
2. It may be that your structure is very strained, or the template
information strongly disagrees with the disulfide you've added, so that
the disulfide restraints cannot be satisfied. In that case, you should
see the violations of these restraints in your log file.