On 7/16/13 12:15 PM, Rohitesh Gupta wrote: > I am trying to model a protein using a template that is 85% similar to > it, but also wants to transfer ligand from another protein that is 10% > similar.
That should be fine - just give an alignment of the three sequences, looking something like
templ1 AAAAAAAA---* templ2 ------BBBB.* target xxxxxxxxxx.*
Ideally you want to take some of the protein from the second template (rather than just the ligand) so you get the ligand-protein interactions correct. And ideally you want a bit of overlap between the two templates.
> This code runs fine but the ligand doesn't have any of the above > mentioned restraints. > How could one instruct modeller to consider these restraints?
Your script looks fine. What makes you think the ligand "doesn't have" any of the restraints? Modeller tries to satisfy *all* restraints (user-added restraints aren't treated specially) so if there's a conflict, you may end up with them not being satisfied.
> I understand that modeller would by default consider the non-bonded > interaction between ligand and the catalytic site amino acids. In such > case, is there a way to override those interactions?
Sure, you can add one or more excluded pairs. See http://salilab.org/modeller/9.12/manual/node108.html You can just add these in the same special_restraints method.
Ben Webb, Modeller Caretaker