Compiling ChimeraX

The source code is at GitHub RBVI/ChimeraX repository with instructions for getting it here.

ChimeraX depends on over 50 third-party packages so it can be challenging to build. We recommend using production releases or daily builds from the ChimeraX download page instead of compiling it yourself.

ChimeraX has been built on Windows 10, macOS 10.12 through 10.15, and Linux (RedHat / CentOS 7 and 8, Ubuntu 20,18,16). ChimeraX is coded in Python (currently version 3.7) and C++.

A build is done using make by running

make install

in the top-level directory of the ChimeraX source code. This compiles third party-prequesite packages such as Python 3, and installs many needed third party packages from PyPi using “pip install”. It also installs various non-Python third-party libraries. It builds wheels for about 100 ChimeraX-specific bundles written in Python and C++. And it builds an application with an appropriate directory structure the operating system.

None of these operations leak out of the built ChimeraX and onto the rest of the system.

The ChimeraX build as of October 2022 uses commercial PyQt6 (through a hand-rolled Qt shim) for the Qt user interface.

The prereqs subdirectory contains Makefiles to build the various third party packages. Most of the ChimeraX build time is making these prereq packages. To save time on subsequent builds the installed packages are archived in a file prereqs/prebuilt-<OS>.tar.bz2.

Nightly Builds

Nightly builds on Mac, Windows and Linux are build with scripts in the ChimeraX git repository build_tools on plato.cgl.ucsf.edu.

Windows Build

Microsoft Visual Studio Community 2017 or 2019 is used to compile C++ on Windows. This compiler was chosen to match the compiler used by the standard Python 3 distribution.

Cygwin is use to provide a unix-like environment (bash shell, make, …) to build ChimeraX on Windows.

Steps for compiling ChimeraX on Windows 10:

  1. Install Microsoft Visual Studio 2019 Community Edition:

    Select components
  "Desktop Development with C++".
  "Universal Windows Platform development".

The ChimeraX setup script vsvars.sh uses old versions of some components
that you will need to choose from the installer "Individual Components"
section
  Windows 10 SDK version 10.0.18362.0
  MSVC v142 - VS 2019 C++ x64/x86 build tools (v14.24)
Alternatively you can edit the vsvars.sh script to use the current
Visual Studio 2019 versions of these components.

Then start Visual Studio and login, then quit, to complete setup.

  2. Install Cygwin, 64-bit version. In addition to the default packages, you’ll need:

    binutils - xdr in md_crds needs ld.exe
git - to be able to check in changes
Imagemagick - to create icon files
make - to run the build process
openssh - to get network access to plato
patch - to patch source distribution
rsync - to install files and fetch them
unzip - used to build ffmpeg

  3. Clone the ChimeraX repository from GitHub.

  4. Run “. ./vsvars.sh” in chimerax root directory to set path to Visual Studio compiler. If you use different Microsoft SDK or build tools versions then you will need to edit the vsvars.sh script to use your versions. If you do not it will not give any errors but all compilations will mysteriously fail.

  5. “make install” in the repository root.

Linux Build

All of the binary Linux ChimeraX bundles are built on a lowest common denominator (LCD) Linux. That way a Linux binary download from the toolshed will work on all Linux variants. The only code specific to a Linux variant is the Python binary and dependencies (especially OpenSSL, so it gets security patches from the vendor), and the AmberTools binaries that have a FORTRAN runtime dependency.

The RBVI uses singularity/apptainer containers for each supported Linux variant. The Linux variant specific singularity definition files can be found in the linux_buildenv directory. At the time of this writing, ChimeraX uses Rocky 8, a Red Hat Enterprise Linux derivative, as the LCD Linux.

macOS Build

XCode compilers are used. Tested with XCode version 12.2 (Jan 2021) on macOS 10.15 (Catalina) and 11 (Big Sur).

  1. Clone the ChimeraX repository from GitHub:

    git clone git@github.com:RBVI/ChimeraX.git chimerax

  2. There may be some build tools or libraries needed from Homebrew. We need to start with a clean machine to figure out what is needed. Known dependencies can be installed by running the following command from the chimerax directory.

    brew bundle

  3. In the repository chimerax directory run make to build the application:

    make build-from-scratch >& make.out

Known Issues

  • On macOS Monterey with Anaconda bin directory /opt/anaconda3/bin in the PATH the the ChimeraX lxml compilation can find the incorrect Anaconda lxml header files resulting in broken lxml the missing symbol _xmlFree. Lxml is used by bundle builder and will fail building ChimeraX bundles. A workaround is to temporarily remove Anaconda from PATH.