Hi, I?m trying to do a joint RDC/SAXS refinement of a docked protein complex and running into problems with the RDCs during the rigid-body dynamics.
Basically, I put the saxs and rdc calls from saxsref/anneal.py into diffTens/dock/dock.py. During refinement, the dock_xx.sa files have very high rdc energies (40,000 kcal/mol, 100 violations), but the dock_ave.pdb has very low energies (100 kcal/mol, 2 violations). I?m using rdc-refined structures as docking modules, so they should give low energies, even if held rigid. The structures of the dock_xx.sa and dock_ave.pdb are very close to each other (not surprising given rigid body docking), but the principal axes point in different directions. RDC calculation using calcTensor also shows that the xx.sa structures don?t fit the RDCs as well as the ave.pdb. It seems as though the protein and the rdc tensor are both being held rigid except for during the minimization of the average structure (which looks to be non-rigid body). I?ve appended rdcs to all of the potLists, so they appear to be in use during the refinements. Should they be defined in dyn_fix.fix (or dyn_free_sch.group, etc.)? I have protocol.torsionTopology(dyn_fix,oTensors=media.values()) and protocol.torsionTopology(dyn_free_sch,oTensors=media.values()) statements (and I?ve tried with and without the oTensors). Thanks, David David A. Horita, Ph.D. Department of Biochemistry Wake Forest University School of Medicine Winston Salem, NC 27157, USA
