Reply To: Modeling circular permutation and domain insertion

[Anonymous]

What you really want to do is loop modeling, where the domain insert is treated as a big fixed portion of loop (no internal degrees of freedom changed). This is not possible without modifying the loop modeling code. If you go in and change how the MoveMaps are set up to fix the conformation your inserted domain, you can do CCD loop modeling (and with some more work, KIC too). I can point out the functions to work with if you want to try this, but I can’t write the code for you.

Failing that, you can try Relax mode. You can write a constraint file (http://www.rosettacommons.org/manuals/archive/rosetta3.2.1_user_guide/constraint_file.html) that includes a DihedralConstraint for each torsion in the core of your protein, and in the inserted domain, but no constraints on the “loop” residues. Relax mode will try to model all residues, which is inefficent, but the constraint will prevent it from making changes outside the loop region. This is likely to be very slow compared to code written for the purpose, but it’s the only thing I can think of that you can do in 3.2.

There may be a way to do it with the abinitio “broker” code in 3.2 but there is no documentation for it.