chimerax-clipper

Clipper plugin to ChimeraX, for handling of crystallographic maps and symmetry

A modified and extended version of Clipper-Python based on Kevin Cowtan's Clipper Library for use as a plugin to UCSF ChimeraX. Primarily built for use with ISOLDE, but other uses are welcomed.

Building

First of all, make sure you need to! Release builds of ChimeraX-Clipper can be installed directly from ChimeraX's ToolShed (Tools/More Tools...), and development builds are released semi-regularly. If you still want to build your own:

• Download and install a compatible version of ChimeraX (see the "ChimeraX-Core" entry in the Dependencies section of https://github.com/tristanic/chimerax-clipper/blob/master/bundle_info.xml for the current version restrictions).
• Make sure you have the correct compiler: for Linux, you'll need to build using the same toolchain as was used to build ChimeraX itself (currently gcc-toolset-10 in RHEL 8). A Singularity recipe for their build environment can be found at https://github.com/RBVI/ChimeraX/blob/develop/prereqs/linux_buildenv/rhel-8.def. For MacOS you'll need XCode, and for Windows you'll need Visual Studio (ideally 2019, but newer versions tend to be good about maintaining backward compatibility).
• In Linux or MacOS, setting the environment variable RELEASE=1 will cause the Makefile to use the chimerax executable in Linux (assumed to be on the path), and /Applications/ChimeraX.app/Contents/bin/ChimeraX in MacOS. If the RELEASE environment variable is not set, then it will instead use chimerax-daily in Linux, and /Applications/ChimeraX_Daily.app/Contents/bin/ChimeraX in MacOS.

make clean
make app-install

• Since the documentation is generated using Sphinx, it needs to be generated after you've already installed the bundle once. To regenerate and install the documentation, run:

make docs
make app-install

• In windows, "make" is only available in a CygWin or MinGW environment. To build from the Windows console, use the make_win.bat and make_docs.bat batch files:

make_win {release} clean app-install
make_docs {release}
make_win {release} app-install

If "release" is included, then building will use c:\Program Files\ChimeraX\bin\ChimeraX-console.exe, otherwise it will use c:\Program Files\ChimeraX-Daily\bin\ChimeraX-console.exe. Restart ChimeraX before using the plugin.