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I'm having trouble re-designing a 2-component symmetric nanoparticle with small gaps along lines that connect symmetry axes. The starting pdb looked good, so I selected 2 chains that define the unit cell and apply a symmetry file to enable the computational savings associated with symmetry. However, the symmetric docking step that's triggered by the rosetta.protocols.symmetry.SetupForSymmetryMover method seems to smush the chains together, resulting in a smaller radius nanoparticle with VdW clashes.
I am new to MPI so please correct any misuse of terms. My question is about optimizing for MPI on an HPC or a second (preferred) solution to my issue is to optimize my RAM usage so I don't have to run MPI, serial would actually improve overall models produced anyways.
I would like to run a design protocol on a protein that has, as its asymmetric unit, 2 proteins with an ion. I have done some purely AA-based symmetric design before with 2 chains controlled by separate virtual jumps and my own python-generated symdef file but I'd rather avoid doing that again :-)
My hope was that I could put (even if suboptimal) the 2 chains and the ion in a single chain and proceed as usual in symmetric design with one chain.
I'd like to do something similar to regular Rosetta fold-and-dock but in PyRosetta. I've looked at D060_Folding.py and D100_Docking.py examples and while I (mostly) understand what each is doing, I have no idea how to combine them.
How to get a foldtree with symmetry? (in my case it's just simple C3)
How to combine folding and docking? Just alternate calls to folding.apply(test_pose) and dock_prot.apply(test_pose)? (It can't be that simple...)
I'd like to fold-and-dock a trimeric transmembrane domain. I mostly have the "Fold And Dock" working following the example in demos/public/symmetry_examples/fold-and-dock/. However this is treating the transmembrane helixes as though they are in solvent (so for example any hydrophilic groups always rotate outwards). I'd like to do something which is a combination of "Membrane Abinitio" and "Fold and Dock". Is this possible, and how do I do it?