Macs in Chemistry

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Installing Osprey 3.0 under Mac OS X

A recent publication described OSPREY 3.0: Open-Source Protein Redesign for You, with Powerful New Feature DOI.

We present Osprey 3.0, a new and greatly improved release of the osprey protein design software. Osprey 3.0 features a convenient new Python interface, which greatly improves its ease of use. It is over two orders of magnitude faster than previous versions of osprey when running the same algorithms on the same hardware. Moreover, osprey 3.0 includes several new algorithms, which introduce substantial speedups as well as improved biophysical modeling. It also includes GPU support, which provides an additional speedup of over an order of magnitude. Like previous versions of osprey, osprey 3.0 offers a unique package of advantages over other design software, including provable design algorithms that account for continuous flexibility during design and model conformational entropy. Finally, we show here empirically that osprey 3.0 accurately predicts the effect of mutations on protein–protein binding.

Osprey 3.0 is available at http://www.cs.duke.edu/donaldlab/osprey.php as free and openā€source software GPLv2.

The source code is available on GitHub https://github.com/donaldlab/OSPREY3/.

Unfortunately the installation instructions do not include Mac OSX but there are instructions for "Debian-like Linux" which seemed promising. With the invaluable help of Nathan Guerin I was able to get OSPREY installed.

The prerequisites are 64bit, Python 2.7 and the latest version of Java.

I have both python2 and python3 installed on my machine but typing the following conformed that python 2.7 was installed.

MacPro:~ Chris$ python2
Python 2.7.13 (default, Aug 22 2017, 12:42:29) 
[GCC 4.2.1 Compatible Apple LLVM 8.1.0 (clang-802.0.42)] on darwin
Type "help", "copyright", "credits" or "license" for more information.

And it looked like I had Java 8 installed

MacPro:~ Chris$ /usr/libexec/java_home -V
Matching Java Virtual Machines (1):
    1.8.0_73, x86_64:   "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home

Installing OSPREY

To install OSPREY first download and un-tar the latest Osprey3 release (https://github.com/donaldlab/OSPREY3/releases/download/v3.0b1/osprey-python-3.0-beta1.zip)

Then in the root of the extracted directory, open “install.sh” in a text editor (I used BBEdit) and remove the “--use-wheel” flag and then re-save the file.

Open a Terminal window in the extracted directory and type, the install scripts use pip internally to install the Python package

run "./install.sh"

Incidentally, there is a very useful shortcut open System Preferences and select Keyboard > Shortcuts > Services. Find "New Terminal at Folder" in the settings and click the box.

TerminalAtFolder

Now when you control-click (or right-click) there is an option in the "Services" section of the dropdown menu to open a Terminal window at the folder.

We can now start OSPREY

>MacPro:~ Chris$ python2
Python 2.7.13 (default, Aug 22 2017, 12:42:29) 
[GCC 4.2.1 Compatible Apple LLVM 8.1.0 (clang-802.0.42)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import osprey
>>> osprey.start()
No Java runtime present, requesting install.

Screenshot 2018-11-28 at 07.58.28

After some discussions we decided to install the latest version of the Java 8 JDK from Oracle. https://www.oracle.com/technetwork/java/javase/downloads/jdk8-downloads-2133151.html

After which

MacPro:~ Chris$ /usr/libexec/java_home -V
Matching Java Virtual Machines (2):
    1.8.0_192, x86_64:  "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_192.jdk/Contents/Home
    1.8.0_73, x86_64:   "Java SE 8" /Library/Java/JavaVirtualMachines/jdk1.8.0_73.jdk/Contents/Home

/Library/Java/JavaVirtualMachines/jdk1.8.0_192.jdk/Contents/Home

I tried the above instructions and got the same error, I then restarted my Mac and tried again, and SUCCESS!

MacPro:~ Chris$ python2
Python 2.7.13 (default, Aug 22 2017, 12:42:29) 
[GCC 4.2.1 Compatible Apple LLVM 8.1.0 (clang-802.0.42)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import osprey
>>> osprey.start()
OSPREY 3.0-beta1
>>>

I'll have a more detailed look at Osprey in the future.

Last Updated 3 December 2018