Hi, I'm trying to use rosetta holes to design a well packed 4-helix bundle around a Zn porphyrin. I'd like to use the hole_min energy weight to bias the design toward a well packed structure. It seems I want to increase the cavity probe radius, since holes does not seem to penalize the structures for very widely separated helices (i.e., a water molecule can definitely get in between the helices, so holes doesn't seem to penalize this, but I'd like it to.) So I'd like to increase the probe radius, and have holes (or packstat) rescore the structure accordingly. However, the holes and packstat score seem to be independent of cavity probe radius. The output pdb files do change (if I increase the probe radius, the holes output pdb had a larger number of surface cavities), but not the score. Here's the command line example for packstat and holes that I'm running:
~/rosetta/rosetta-3.5/rosetta_source/bin/packstat.default.linuxgccrelease -database ~/rosetta/rosetta-3.5/rosetta_database/ -s ../initial_design_noloops.pdb -extra_res_fa ../PZNF.params -cavity_burial_probe_radius .1 -constant_seed -jran 1111111 -min_surface_accessibility 0
~/rosetta/rosetta-3.5/rosetta_source/bin/holes.default.linuxgccrelease -dalphaball ~/DAlphaBall_new/src/DAlphaBall.icc -database ~/rosetta/rosetta-3.5/rosetta_database/ -holes:make_pdb -holes:make_voids -s flexback5initial_design_noloops_0001.pdb -extra_res_fa ../PZNF.params -packstat:cavity_burial_probe_radius 3 -constant_seed -jran 1111111
The cavity_burial_probe_radius and min_surface_accessibility options do not affect the holes score or packing score in any way. It doesn't matter if I change these values to 0, 1 or 100. Is this to be expected? Is there a way that I can change this?
I talked to Will Sheffler about it, and he indicated that he's should be in touch with you regarding your RosettaHoles issues.
P.S. It's fine for debugging purposes, but once you start to do production runs you'll want to get rid of the "-constant_seed -jran 1111111" flags, or at the very least change the "1111111" to something different for each execution.