local refinement

I am attempting to understand the docking protocol used in Rosetta and the flags to control various phases. From the 2003 JMB paper: ” In the first stage of the algorithm, we employ a rigid-body Monte Carlo search, translating and rotating one partner around the surface of the other through 500 Monte Carlo move attempts. Step sizes are adjusted continually to maintain a 50% move acceptance rate, with initial Gaussian perturbation sizes of mean value 0.7 Å (along all three axes) and 5° (spin around the axis of protein centers and tilt off this axis in a randomly-chosen direction). “

Is this (Low resolution search) the phase controlled by the -docking:dock_mcm_trans_magnitude and -docking:dock_mcm_rot_magnitude flags?

Or do the flags refer to the next (High resolution) phase: “…Once the proteins have side-chains, the rigid-body displacement is optimized….To simultaneously optimize the side-chain conformations and the rigid-body position, the side-chain packing and minimization operations are repeated 50 times (Figure 2). Before each cycle, the position of one protein is perturbed by random translations of mean 0.1 Å in each direction of Cartesian space and by random rotations of mean 0.05° around each Cartesian axis. “

1) Basically, do the -dock_mcm_trans/rot_magnitude flags set the perturbation size for the Low-resolution or High-resolution phase? The default values for these flags are listed as (0.1 Å and 5° respectively). This is a little confusing because it does not exactly match either set of default values listed in the paper: Low-Resolution (listed as 0.7 Å and 5° in the paper) or High-resolution (listed as 0.1 Å and 0.05°)? Were the default values changed?

2) Finally, my understanding is that -dock_pert 3 8 would simply add a random perturbation of 3deg, 8angstr in any direction before the start of the Low-resolution phase. Whereas -docking_local_refine would skip the low resolution phase entirely and simply carry out the High-resolution phase. Is this correct?

3) I am interested in adjusting the perturbation size for the High-Resolution phase. If the -dock_mcm_trans/rot_magnitude flags turn out to control the Low-resolution phase, then is there a way to adjust the perturbation size for the High-resolution phase?

Thank you for your time. I would appreciate any feedback.