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
Written by Emily Koo and Michael Pacella (Graylab), firstname.lastname@example.org
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
Simultaneous optimization of protein rigid-body orientation, backbone and side chain conformations on a solid surface.
cd rosetta_inputs/Osteocalcin demo
Before running the scripts for the first time, make sure that all the following details are addressed.
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:
Create/open .bashrc in home directory
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
Add all directories containing scripts to end of PATH statement, delimited by a colon
where /path/to/scripts and /path/to/more/scripts should be modified to the correct directories.
Make sure that the SetPyRosettaEnvironment.sh is sourced every session. Add
Save and close file, then source it.
:wq source ~/.bashrc
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/*
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.
To generate plots, simply run:
Make sure that the folder contains either only adsorbed state PDBs (and native.pdb) or solution state PDBs.
(in the directory with output decoys)
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
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