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.