You are here

Membrane

Relax in membrane pull my protein out of the membrane

Category: 
Membrane

Good day, 

I am having issues with the mp_relax protocol. I am testing the protocol directly from a PDB crystal structure, and the relax algorithm takes this structure out from the membrane region (as defined by the MEM residue). I am first optimizing the membrane location with the mp_transform (with the -mp:transform:optimize_embedding true option), which positions the protein in the membrane as expected. Then, the relax protocol pulls out the protein from this "correct" membrane position, leaving the protein completely exposed to solvent.

Post Situation: 

calcium metal nomenclature: Rosetta_cm confusing HETATM CA (calcium) with ATOM CA (alpha-carbon)

Category: 
Structure prediction
Constraints
Symmetry
Membrane

Dear community,

I had this posted under a different sub-forum but I realized it didn't fit that forum so deleted it and reposting here.

Post Situation: 

MPI optimization on TACC stampede2 HPC

Category: 
Structure prediction
Loop Modeling
Symmetry
Membrane

Dear community,

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.

Post Situation: 

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!

Category: 
Membrane

I am doing an efficiency analylis on the different minimization options in Rosetta using FastRelax, MPRelax and lbfgs_armijo_nonmonotone minimizer on a membrane protein using the franklin2019 score function and I very very often get this error:

core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!

Post Situation: 

Membrane-bound relaxation constrained by an ED map

Category: 
Membrane

I am energy minimising a membrane protein with the RosettaMP framework, but also constraining it to the electron density map.

I am creating the membrane chain vector thinggy by starting with an OPM database style PDB (protein placed ±14 Å xy plane but without the cute membrane marker atoms aren't used) with the usual `pyrosetta.rosetta.protocols.membrane.AddMembraneMover('from_structure')`, but then I am calling `pyrosetta.rosetta.protocols.simple_moves.AlignChainMover()` to move the pose (based on the peptide chain) to a pose in the ccp4 map.

Post Situation: 

OptimizeMembranePositionMover - This element is not expected

Category: 
Membrane

Hello,

I am receiving the following XML validation error when implementing OptimizeMembranePositionMover: 

Error messages were:
From line 11:
Error: Element 'OptimizeMembranePositionMover': This element is not expected.

Post Situation: 

Pages

Subscribe to RSS - Membrane