The scripts and input files that accompany this demo can be found in the demos/protocol_captures directory of the Rosetta weekly releases.

This is a protocol capture, and represents the protocol at a fixed point in time. It may not work with the current version of Rosetta.

KEYWORDS: SURFACES GENERAL

Authors

Written by Emily Koo and Michael Pacella (Graylab), mpacella88@gmail.com

General Description

This demo will describe how to run the PyRosetta version of the RosettaSurface algorithm. The test case shown here will analyze the adsorption of the biomineralization protein osteocalcin to the 100 surface of the mineral hydroxyapatite

Algorithm

Simultaneous optimization of protein rigid-body orientation, backbone and side chain conformations on a solid surface.

Commands

  1. cd rosetta_inputs/Osteocalcin demo
  2. surface_docking.py@flags

Input Files

  • 1Q8H100.pdb = input pdb file, extended osteocalcin positioned above HAp 100
  • 1Q8H_disulf = disulfide bond specification file
  • 1Q8H_native.pdb = native crystal structure of osteocalcin
  • aa1Q8H_03_05.200_v1_3 = 3mer fragments for osteocalcin
  • aa1Q8H_09_05.200_v1_3 = 9mer fragments for osteocalcin
  • flags = arguments for rosetta surface

PyRosetta RosettaSurface Setup and Pre-processing

Before running the scripts for the first time, make sure that all the following details are addressed.

  1. When PyRosetta is installed, the install directory may be different from user to user, so adding the scripts directories to the PATH environment variable in .bashrc file will allow the scripts to be run from any directory, independent from the actual location of the scripts. The following instructions show how the directories are added:

    1. Create/open .bashrc in home directory 

      vi ~/.bashrc

    2. If file exists, skip to 3. Else, add the following lines to the file: 

      # .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
    . /etc/bashrc
fi

export PATH=$PATH

    3. Add all directories containing scripts to end of PATH statement, delimited by a colon 

      export PATH=$PATH:/path/to/scripts:/path/to/scripts/pdb_objects/
      where /path/to/scripts and /path/to/more/scripts should be modified to the correct directories.

    4. Make sure that the SetPyRosettaEnvironment.sh is sourced every session. Add 

      source /path/to/PyRosetta/SetPyRosettaEnvironment.sh

    5. Save and close file, then source it. 

      :wq
source ~/.bashrc

  2. Make sure the python and bash scripts are given the permission to be executed. Run the following command in the directory containing the scripts 

      chmod +x *.py *.sh ./pdb_objects/*

  3. Gnuplot is the plotting program used to generate the plots, so the program path has to be modified in each Plot* file for the plots to be generated automatically. The version used is 4.2.

  4. To generate plots, simply run: 

      PostProcessRS.sh
    Make sure that the folder contains either only adsorbed state PDBs (and native.pdb) or solution state PDBs.

Post-processing

(in the directory with output decoys)

  1. GetTop.sh Ads 4
  2. cd TOP4.Ads
  3. PostProcessRS.sh

These commands will extract the top 4 adsorbed-state decoys for analysis and generate secondary structure, protein-protein contact maps, and protein-surface contact maps

Example output:

  • Ads_SecStruct.png = adsorbed state secondary structure
  • Sol_SecStruct.png = solution state secondary struccture
  • Ads_ContactMap = adsorbed state contact map
  • Sol_ContactMap = solution state contact map
  • Surface_ContactMap.png = protein-surface contact map
  • Diff_ContactMap.png = difference map between contacts in the ads/sol state

Limitations

This app requires a single protein positioned above a solid surface whose parameters are present in Rosetta. The protein needs to appear before the surface in the pdb file and the two need to be separate chains