You are reading the documentation for version 1.6 of OpenStructure. You may also want to read the documentation for: 1.1 1.2 1.3 1.4 1.5 devel

Installing OpenStructure From Source


This document describes how to install OpenStructure from source. If you are mainly insterested in using OpenStructure and are not planning to modify the code of OpenStructure itself, please use one of the binaries available for download.

Brief Overview

Compiling OpenStructure consists of several steps that are described below in more detail. In essence, these steps are:

  • Installing the Dependencies
  • Checking out the source code from GIT
  • Configuring the build with cmake
  • Compiling an Linking

Installing the Dependencies

OpenStructure uses a bunch of OpenSource libraries. If you haven’t already installed them, please install them now! Where appropriate the minimally required version is given in parantheses.

When you enable support for image processing, you will need:

  • FFTW3. By default, OpenStructure is compiled with single precision and thus also requires FFTW to be compiled with single precision. Most platforms offer this as a second package. If you are compiling manually, use the –enable-single option.
  • libtiff

If you would like to use the graphical user interface, also install:

In case you are compiling under Windows you have to install Visualstudio 2008. to compile the dependencies and OpenStructure. We recommend to compile the dependecies manually. Enter the directories where the dependencies are located in Tools->Options->Projects and Solutions->VC++ directories. Choose ‘bin’ directories to enter program paths to cmake, qmake and python, ‘lib’ directories to point to the location(s) of your dependencies.

Getting the Source Code

OpenStructure uses git as the revision control system. The main repository can be browsed here. To get the source code, use git clone:

git clone <directory-name>

The above command will clone OpenStructure into the directory called directory-name. If omitted, the directory will be called ost.


Some versions of curl have have trouble with the certificate of the OpenStructure git server and fail to clone the repository. To work around this, disable the SSL certificate verification by setting the following environment variable:


Picking the right branch

By default you are checking out the master branch. Master is, by definition a stable branch. It always points to the latest release. However, there are several other branches at your disposal. The main development is happening in the develop branch. It contains the newest features and bug fixes. However, we dont’t make any guarantees that the develop branch is bug free and doesn’t contain major bugs. After all, it’s in constant flux. If you are developing new features, start your feature branch off develop. Besides that, there are several smaller features branches that are used to group together commits for one specific features. To change to a specific branch, use

git checkout <branch-name>


OpenStructure uses CMake for compiling and building the project. The next required step is to configure the build environment using cmake. You can do that by invoking cmake in the project directory.

cmake . <options>

There are two kinds of options: Options that let you control the building behaviour, enabling and disabling the compilation of certain modules and options that let you tell CMake where to find the dependencies. All of them are passed to CMake with via -D<opt>=<value>.

On Windows, use Tools -> VisualStudio -> commandline prompt from within VisualStudio

Flag to choose build generator

CMake supports different build generators. On UNIX, i.e. MacOS X and Linux, the default build generator is Makefiles, but it is also possible to use other programs. For a list of supported build generators on your platform, start cmake without parameters.

On Windows you have to explicitly set the build generator to “Visual Studio 9 2008”(or a later version):

cmake -G"Visual Studio 9 2008"

Flags to Control the Dependencies

By default, CMake searches the standard directories for dependencies. However, on some systems, this might not be enough. Here is a short description of how CMake figures out what dependencies to take and how you can influence it.

  • Boost is mainly controlled via the BOOST_ROOT option. If boost wasn’t found, it should be set to the prefix of the boost installation.
  • QT_QMAKE_EXECUTABLE defines the exact Qt installation to take. It should be set to the full path to qmake.
  • PYTHON_ROOT is the Python equivalent of BOOST_ROOT. It should be set to the prefix path containing the python binary, headers and libraries.
  • SYS_ROOT controls the general prefix for searching libraries and headers. By default, it is set to /.
  • COMPOUND_LIB specifies the location of the compound library and activates the rule-based-builder. The compound library is based on the component dictionary released by the PDB, and it specifies atoms of a certain residue or connectivities between atoms etc. The compound library itself is created from the component dictionary by calling the OpenStructure chemdict_tool. By default this is switched off.
  • COMPILE_TMTOOLS will activate bindings for TMAlign and TMScore, which are then available at python level. This option requires a Fortran compiler. By default this option is switched off.
  • USE_NUMPY allows OpenStructure to pass back data in NumPy format. By default this is switched off.

Build Options

  • ENABLE_GUI controls whether to build the graphical user interface module. By default it is set to true.
  • ENABLE_IMG controls whether to build the image processing module. This will enable support for density maps, and general image processing in 1, 2 an 3 dimensions. By default it is set to true.
  • ENABLE_GFX controls whether to build the graphics module. By default, this is set to true. If set to none, this implies ENABLE_UI=NO.
  • Shader support is controlled with USE_SHADER. By default, no shaders are used.
  • If OPTIMIZE is set to 1, an optimized version of OpenStructure is built.
  • PREFIX specifies the location on the file system where to install OpenStructure
  • USE_DOUBLE_PRECISION will switch on double precision within OpenStructure. By default this is switched off.
  • ENABLE_STATIC allows some parts of OpenStructure to be statically linked and thus can be used more easily across a heterogeneous setup, e.g. older systems and newer systems.

Example Configurations

Ubuntu 10.04 Lucid/Lynx

All the dependencies can be installed from the package manager and are thus located in standard locations. cmake will automatically find them without the need to pass any additional parameters. The only exception is -DOPTIMIZE, which will tell cmake to build an optimized (-O3 -DNDEBUG) version of OpenStructure.

cmake . -DOPTIMIZE=1

MacOS X with MacPorts and optimization turned on

MacPorts installs all the software under /opt/local. Thus we have to tell cmake where to find Boost, Python and Qt.

cmake . -DBOOST_ROOT=/opt/local -DPYTHON_ROOT=/opt/local \
      -DSYS_ROOT=/opt/local -DQT_QMAKE_EXECUTABLE=/opt/local/bin/qmake \

Building the Project

Type make. If you are using a multi-core machine, you can use the -j flag to run multiple jobs at once.

On Windows run ‘Build OpenStructure’ from the build menu.

What’s next?

On Linux and MacOS X, you can start dng from the command-line. The binaries are all located in stage/bin:


or, to start the command-line interpreter:


If you repeatedly use OpenStructure, it is recommended to add /path/to/ost/stage/bin to your path.

Getting the newest changes

To get the newest changes from the central git repository, enter

git pull

in your terminal. This will fetch the newest changes.



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