Vikram K. Mulligan

GenKIC should be fully configurable from PyRosetta. I know that @weitzner has done it. The current GenKIC tutorials (https://www.rosettacommons.org/demos/latest/tutorials/GeneralizedKIC/generalized_kinematic_closure_1, https://www.rosettacommons.org/demos/latest/tutorials/GeneralizedKIC/generalized_kinematic_closure_2, https://www.rosettacommons.org/demos/latest/tutorials/GeneralizedKIC/generalized_kinematic_closure_3, https://www.rosettacommons.org/demos/latest/tutorials/GeneralizedKIC/generalized_kinematic_closure_4) are for RosettaScripts, but there's an almost 1:1...

Nice! Thanks, Jordan! On Wed, Dec 25, 2019, 4:09 AM Jordan Willis, wrote: > Here is genkic in pyrosetta > > > https://github.com/jwillis0720/PyRosetta_helper/blob/master/tutorial/GK_Demo.ipynb > < > https://github.com/jwillis0720/PyRosetta_helper/blob/master/tutorial/GK_Demo.ipynb > > >...

>The intention of the system document https://docs.dwavesys.com/docs/latest/doc_handbook.html is to always provide the current best practices in using the D-Wave system and formulating suitable models, and problems to be aware of...

There's no tutorial on designing cyclic peptides with PyRosetta because that's not what we've used for this purpose in the past. The 2017 Hosseinzadeh _et al._ paper has all of...

> I'm wondering if there's a way you can keep the current behavior with the command lines which currently work, but add in support for the additional behavior if you...

This could conceivably fix longstanding bugs with read-in of cyclic peptides from multi-chain PDB files.

One thing that could cause this would be if the disulfide bond has not been declared between residues 166 and 157. Note that GenKIC only moves geometry, and doesn't alter...

Oh, I see the problem. Psi of residue 166 and phi of residue 157 are not part of the loop to be closed, since you're closing through a disulfide. Just...