On 11/26/18 2:22 PM, Luca Jovine wrote:
However I just tried what you suggested - shifting the alignment so that one of the two Cys of a pair is no longer aligned with the template -, but what happens is that the Cys pairs that I specified as making an alternative disulfide using special_patches are now not bonded
You will probably need to experiment a little bit with different alignments. You'll need to be careful not to change the alignment so much that it implies a structure that is inconsistent with the disulfides you want to impose.
Ben Webb, Modeller Caretaker -- modeller-care@salilab.org https://salilab.org/modeller/ Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage