François Sampieri wrote: > I want to force a non-proline peptide bond to the cis configuration in > a 64-residue model.
That should be fine - there's no requirement that the residue is proline.
> I assumed that it would not make a difference if the residue it applies > to is not an actual proline > and I include the routine in my .py script, but I got only models with > the trans peptide configuration.
The problem is in your script - looks like the models won't include the disulfide bridges you've set up either:
1. You have defined the subclass 'mymodel' twice, once containing a special_patches method (for disulfides) and the second time containing a special_restraints method (for the cis peptide). This won't work - the second 'mymodel' class will simply override the first (so you'll get cis peptide but no disulfides). The simple solution: just remove the second class mymodel(automodel): line, so that both the special_patches and special_restraints methods live in the same 'mymodel' class.
2. After you went to all that trouble to define a 'mymodel' class, you went and used the 'automodel' class at the end of your script! To actually get the changes you made, you need to actually use the mymodel class, i.e. change a = automodel(env, to read a = mymodel(env,
Otherwise, all looks fine to me.
> I noticed only 3 lines in the log file with warnings:
All three of these warnings are normal - you'll see them in almost any automodel run.
Ben Webb, Modeller Caretaker