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Membrane-bound relaxation constrained by an ED map

Submitted by matteoferla on Fri, 2020-10-30 07:25
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.

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PyRosetta - Applications

OptimizeMembranePositionMover - This element is not expected

Submitted by bjharris on Wed, 2020-07-01 23:21
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.

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Rosetta 3 - Applications

Coupled Moves crash with Membrane Protein - residue_edge is undefined for root vertex

Submitted by benhardy on Mon, 2020-06-15 09:33
Category: 
Design
Membrane

Hi All,

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: 

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Rosetta 3 - Applications

Building loop extensions in a membrane protein with Remodel

Submitted by benhardy on Tue, 2020-06-02 08:21
Category: 
Design
Scoring
Loop Modeling
Membrane

Hi All,

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:

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Rosetta 3 - Applications

mp_transform optimize with franklin2019 scoring

Submitted by benhardy on Thu, 2020-05-28 08:35
Category: 
Design
Scoring
Enzyme Design
Membrane

Hi All,

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:

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Rosetta 3 - Applications

Transmembrane helix fold-and-dock?

Submitted by sarah_b on Tue, 2020-05-12 02:09
Category: 
Structure prediction
Docking
Symmetry
Membrane

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?

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Rosetta 3 - Applications

alignblast.pl truncated file

Submitted by rlwoltz on Mon, 2019-03-11 18:32
Category: 
Membrane

Hi all,

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:

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Rosetta 3 - General

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