Utilities with Options from RosettaMP

Metrics.cc

Description

This file contains protocols that are specific to low resolution docking.

metrics.cc lives in main/source/src/protocols/docking/metrics.cc

Flags / Options

Flag	Description
`-mp::setup::spanfiles <spanfile>`	Add this option before calculating interaction energy to calculate energy for membrane proteins.

Util.cc (Temporary)

Description

This file contains utility functions for RosettaMP.

This util.cc lives in main/source/src/core/conformation/membrane/util.cc

Flags / Options

Flag	Description
`-mp::setup::spanfiles <spanfile>`	Add this option to read in user-specified spanfile.

Util.cc

Description

This file contains several groups of utilities for working with RosettaMP:

Calculate RMSD between the transmembrane domains of two poses (with or without superimposition)
Calculate the tilt of the protien relative to the membrane normal
Safety checks and convenience methods for working with membrane foldtrees
Utility for accessing DSSP secstruc and z coordinates
Calculate protein embedding based on the structure
Split topology by jump, and other multi-chain (or partner) functions

This util.cc lives in main/source/src/protocols/membrane/util.cc

Flags / Options

Flag	Description
`-mp::setup::center <three real numbers defining the center point>`	Set center vector safely when reading from command line.
`-mp::setup::normal <three real numbers defining the normal vector>`	Set normal vector safely when reading from command line.

Contact

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

References

Alford RF, Koehler Leman J, Weitzner BD, Duran A, Tiley DC, Gray JJ (2015). An integrated framework advancing membrane protein modeling and design. PLoS Comput. Biol. - In Press