I am really hoping that I am not asking a dumb question but I cannot
seem to get the restraints to work on my protein. To try and get to
grips with this I am using a target-template sequence identity of 100%.
I have set the secondary structure as is in the known structure but
cannot seem to ‘force’ the restraints through onto the target.
I see only one problem with your script itself, and that should be
unrelated: special_restraints() is called *after* the system topology is
set up, so patching the topology will have no affect there. To add your
disulfide bridges, add those calls to patch() to the special_patches()
method instead.
Note that restraints created in special_restraints() are *added* to the
list of all restraints; they don't replace existing restraints. So, if
there is a conflict between your restraints and the default set of
restraints, Modeller will not be able to satisfy them. In your case,
this effect will actually be at its most pronounced, because you have a
100% identical template, so the template-derived restraints will be
extremely strong. Secondary structure restraints are rather weak, so
they're only likely to work in regions of the structure where you have
low sequence identity (or no template at all).