Lixia Jin wrote: > First try MODELLER. > 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.
Ben Webb, Modeller Caretaker