application_documentation/membrane_proteins/RosettaMP Movers RangeRelax

Getting Started

Build Documentation

Rosetta Tutorials

Rosetta Basics

Rosetta Applications

• Structure Prediction

• Design

• Docking

• Analysis

• Utilities

• Antibody-specific applications

• RNA-specific applications

• Tools

• Full apps list

Rosetta Scripting Interfaces

Development Documentation

Internal Documentation

How to Write Documentation

FAQ

Glossary

RosettaEncyclopedia

Options list

Metadata

Questions and comments to:

• Julia Koehler Leman (julia.koehler1982@gmail.com)
• Rebecca Alford (rfalford12@gmail.com)
• Corresponding PI: Jeffrey J. Gray (jgray@jhu.edu)

Last Updated: 2/8/18

Description

This Mover relaxes a membrane protein by iteratively relaxing ranges of the protein; no ramping required. It is much faster than FastRelax and good for large to very large proteins (tested up to 5250 residues).

Code and Demo

The Mover lives in main/source/src/protocols/relax/membrane/.

RosettaScripts interface

The following options are available within the RosettaScript interface:

native - String - Provide the native PDB file. sfxn - String - Provide the score function weights file name. center_resnumber - Integer - Provide the center residue number. set_tm_helical - bool - Set helical secondary structure in TM region. optmem - bool - Set option to optimize membrane.

Flags / Options

Flag	Description
-mp::transform::optimize_embedding <bool>	Use the scorefunction to optimize the embedding after an initial coarse grained setting.

Reference

RosettaMP is described in

• Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Elazar A, Tilley DC, Gray JJ (2015) An integrated framework advancing membrane protein modeling and design, PLoS Computational Biology (in press)