Open-Source Protein REdesign for You
For an introduction to OSPREY 3.0 and its new features please read this paper (accepted to the Journal of Computational Chemistry, 2018): https://www.biorxiv.org/content/early/2018/04/23/306324
We require everyone who publishes or presents results from OSPREY to please mention the name "OSPREY," and to cite our papers as described in CITING_OSPREY.txt (especially our new paper introducing OSPREY 3.0).
Copyright (C) 2017 Duke University
This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 2 as published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
The full text of the GPLv2 is included in the accompanying LICENSE.txt
Make sure you're running 64-bit Windows. Osprey is not supported on 32-bit Windows.
- Install Python 2.7 x86-64, choose the
Windows x86-64 MSI Installeroption, not Python 3+ or 32-bit version.
- During Python installation, enable the option to
Add python.exe to Path.
- Install Java 8 64-bit, choose the
Windows Offline (64-bit)option, not 32-bit version.
- After installing Java, add the
C:\Program Files\Java\jre1.8.0_151\binfolder to your
PATHenvironment variable. (See how to set the PATH Environment Variable) Be sure to replace the
jre1.8.0_151part with the actual Java installation folder on your computer. Tragically, the Java installer does not do this for you.
- Download the newest Osprey Python release (not the source files) and extract it to your favorite folder.
- Run the
installbatch script to install Osprey.
on Debian-like Linux:
Including distributions like Ubuntu and Mint
Make sure you're running 64-bit Linux. Osprey is not supported on 32-bit Linux.
Install prerequisites:$ sudo apt-get install python2.7 python-pip openjdk-8-jre
Download the newest Osprey Python release (not the source files) and extract it to your favorite folder.
Run the install shell script to install Osprey:$ ./install.sh
The install scripts use
pip internally to install the Python package. If you want to customize
the installation of the python package, you can ingore the install scripts and call
First download the newest Osprey Python release and extract it to your favorite folder. Then call
$ pip2 install osprey --no-index --use-wheel --find-link=wheelhouse
Upgrading from an older version
If you're upgrading from an older installation of Osprey, just run the install script. There's no need to explicitly uninstall the older version.
To uninstall Osprey, use the provided shell script.
on Linux or Mac:
using Python scripts
Python scripting is the preferred way of using Osprey due to its simplicity and flexibilty. To run Osprey from a Python script:
import osprey osprey.start() # run osprey commands, e.g. osprey.printGpuInfo()
For more information about Python scripting with Osprey, see the tutorial at
in the distribution zip or the Python documentation at
- TODO: add links to online docs (eg tutorials, references)
using the command-line interface
The Python interface to Osprey represents a significant improvement in the user interface over the older command-line interface, and new Osprey projects should consider using the Python interface rather than the command-line interface.
However, for backwards compatibility, the command-line interface is still provided, although it may not receive feature updates in the future. It may eventually be removed from Osprey.
To access the command-line interface, download the Osprey Java distribution. Extract it to your favorite folder, then enter the following command into a shell:
$ cd bin $ ./osprey [commands]
[commands] are the Osprey commands you want to run. You can run Osprey without
[commands] and Osprey will print a list of the available commands.
To show the version of your Osprey installation, try:
$ ./osprey version
To run a GMEC-based protein design, try:
$ ./osprey FindGMEC /path/to/config1 /path/to/config2 ...
To show GPU informatino, try:
$ ./osprey GPUInfo
GpuInfo command prints info about available GPUs in the system, and which
ones Osprey can use.
Osprey is open-source software and contributions are welcome.
See the guide for contributors to see how to compile and package Osprey.