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Membrane

mp_transform optimize with franklin2019 scoring

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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Transmembrane helix fold-and-dock?

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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alignblast.pl truncated file

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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Changing the membrane Thickness (THKN)

Category: 
Membrane

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))

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Membrane protein protocol on PyRosetta

Category: 
Membrane

Hello Rosetta community

I need to score a membrane protein using PyRosetta and am having trouble with the implementation.  The 2014 post in the forum has not been very helpful in terms of syntax, and there is little to no documentation. I see a tutorial is in the works on the website, but if anyone has advice right now that would be greatly appreciated. A working (minimal) example would probably be most helpful, something I can work off of. 

Thank you

Joel

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"caught exception" for PDB with membrane "DUM" residues

Category: 
Scoring
Membrane
Non-Canonical Peptides

If I run this command:

residue_energy_breakdown.static.linuxgccrelease -in:file:s hasDUMresidues.pdb -out:file:silent energy_breakdown.out -ignore_unrecognized_res true

on the attached pdb, I get this error:

caught exception 

 

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