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I came across the Coupled Moves protocol recently and it sounds like an interesting alternative to FastDesign that I've been predominantly using. I tried to implement the CoupledMoves Mover within my RosettaScripts design script, however, I keep coming across the following error:
ERROR: FoldTree:: residue_edge is undefined for root vertex
ERROR:: Exit from: src/core/kinematics/FoldTree.cc line: 2317
[0m[0mprotocols.rosetta_scripts.ParsedProtocol: [0m[31m[1m[ ERROR ][0m Exception while processing procotol:
I was wondering whether Remodel is currently compatible with the RosettaMP framework? I have a designed membrane protein and I'm trying to alter the sequence of water-exposed loops, which involves a few insertions. I'm using Remodel to do this but haven't been able to run it using the franklin2019 scorefunction.
Here are the flags that I'm using:
I am running some flexible backbone design on a transmembrane four-helix bundle heme protein via RosettaScripts. I'm finding that the membrane residue is moving a lot during design, and I have to optimize the embedding with mp_transform post-design to reposition the mem residue. I have a few questions about this:
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?
I'm looking for a basic sanity check on how mpi should work with mp_mutate_relax. I've compiled rosetta-2019.47.61047 with extras=mpi and it all seems to be working fine. So if i run mpiexec -np 4 $rosetta3/bin/mp_mutate_relax.mpi.... with the following flags:
I'm a bit of a novice when it comes to programming with only basic training so this problem seems to be a little over my head.
So I know this issue has been addressed before with run_lips4.pl but the resulting solutions for that seem to be either an improper name creation or a blank blast file due to incorrect blast database downloads. While my error seems to be specific to alignblast.pl.
I run run_lips4.pl with the following command:
Hello (Py)Rosetta community
Currently whenever I add a membrane to my pose the membrane thickness is always 15 A (30 total). I would like to elongate that in order to model different types of phospholipids found in bacterial cells.
My best idea to do this is to change the x-coordinate of the membrane residue in the pose object, using the following commands
>>> AID = AtomID(1, pose.size())
>>> pose.set_xyz(AID, XYZ(30,0,0))