What are the degrees of freedom that are minimized when minimizng across a jump? Is it just a rotation (spin) about the jump vector and movement along the vector? I'm working on an interface design probelm and I've set up my movemap where sidechains are allowed to minimize, backbones are held fixed, and jumps are allowed to minimize. I'd like to perform a rigid-body minimization between my two chains and I'm trying to understand which degrees of freedom are minimized.
For example, suppose I have a fold-tree A through D as shown below, where B->C is a jump.
... A->B->C->D ...
Are the only degrees of freedom that are minimized the torsion around A-B, B-C, and C-D, and the vector along B-C?
If so, is there a way to also allow the angle A-B-C and B-C-D to minimize?
Thanks in advance.
A jump represents 6 degrees of freedom (xyz at either end is one way to think of it). All should be free when minimizing a jump. I think this translates, in internal coords, to the pseudobond length, the two pseudobond angles, and the three pseudobond torsions that involve the pseudobond.
If you test and find a problem, let us know!
Great, thanks for the quick reply.