ERRASER

ERRASER (Enumerative Real-space Refinment ASsisted by Electron-density under Rosetta) is an application for improving RNA crystal structures based on Rosetta and Phenix.

Installation

To run ERRASER, you need to have Rosetta and Phenix installed on your machine.

To download and install Rosetta:

Request a license and download the software at rosettacommons.
See the Rosetta installation documentation at rosettacommons.

To download and install Phenix:

Download the software at phenix. Phenix is free for academic users.

Finish setup:

Ensure you have correctly setup Phenix. As a check, make sure the following command works:

phenix.rna_validate

Make sure you have a Python v2.7 (python --version). If not, go to the rosetta/tools/ERRASER/ folder and run:

./convert_to_phenix.python

This will change the default python used by the code to phenix-built-in python, instead of using system python.

Set an environment variable $ROSETTA to the path to Rosetta. If you use bash, append the following lines to ~/.bashrc:

ROSETTA=/path/to/Rosetta/; export ROSETTA;

Also add the ERRASER script folder to your $PATH. Here is a bash example:

PATH=$PATH:/path/to/Rosetta/tools/ERRASER/

Once Rosetta and Phenix have been installed, ERRASER can be run from the command line, e.g.:

erraser.py -pdb 1U8D_cut.pdb -map 1U8D_cell.ccp4 -map_reso 1.95 -fixed_res A33-37 A61 A65 

Demo

For a minimal demonstration of ERRASER, see: Rosetta/demos/public/erraser/. Example input files for the demo can be found at: Rosetta/demos/public/erraser/rosetta_inputs/. Likewise, example output files can be found at: Rosetta/demos/public/erraser/example_output/.

Documentation

Rosetta Documentation is available at rosettacommons.
Phenix Documentation is available at rosettacommons.

License

References

Chou, F.-C., Sripakdeevong, P., Dibrov, S.M, Hermann, T., and Das, R. (2013)
Correcting pervasive errors in RNA crystallography through enumerative structure prediction
Nature Methods 10: 74 - 76. | Paper | Link | Server

Sripakdeevong, P., Kladwang, W., and Das, R. (2012)
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling
Proceedings of the National Academy of Sciences U.S.A. 108 (51) : 20573 - 20578. | Paper | Link

Workflows

I have crystallographic/cryoEM data

Developed by Das lab, Leland Stanford Junior University.

README by Caleb Geniesse, May 2016.