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Re: [modeller_usage] non-proline cis-peptide bonds

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
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage