Installing and Running CCPNMR Analysis 2.5.2 (Portable macOS)

This guide explains how to install and run the portable, self-contained standalone distribution of CCPNMR Analysis 2.5.2 on macOS (modernized for Python 3.14).

The standalone archive is fully self-contained. It embeds its own private Python 3.14 runtime, compiled C/Cython extension libraries, and all required scientific and graphical dependencies. No developer tools, Xcode, or system python configurations are needed.

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Prerequisites

None. The macOS standalone is fully self-contained: it embeds its own private CPython 3.14 runtime together with Tcl/Tk 9.0.4 (native Aqua canvas port — no X11 / XQuartz required). Just download, extract, and run.

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Installation

1. Download the portable tarball (e.g., ccpnmr-2.5.2-macos-arm64-standalone.tar.gz).
2. Extract the archive in your Terminal:

   tar -xzf ccpnmr-2.5.2-macos-arm64-standalone.tar.gz
   cd ccpnmr-2.5.2-macos-arm64-standalone

The archive is built for the architecture of the Mac that built it (Apple Silicon = arm64, Intel = x86_64) — run it on a matching Mac.

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Running the Application

There is no launcher script — the tree is self-contained. Run:

1. Launch the main CCPNMR Analysis GUI (Default)

./bin/analysis                # or: ./bin/analysis /path/to/project

2. NEF import / export (non-GUI)

./runtime/bin/ccpnmr-nef import file.nef [--project-name NAME] [--force]
./runtime/bin/ccpnmr-nef export <project-directory> <output.nef>

The tree reads nothing from and writes nothing to the system except the project you open/save (and your default browser for Project > Summary).

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Installing and Running CCPNMR Analysis 2.5.2 (Portable Linux x86_64)

The Linux standalone distribution is self-contained in the same way: an embedded private CPython 3.14 runtime, the compiled C extensions, and all dependencies. No system Python and no pip are involved at run time.

1. Unpack the standalone archive (e.g. ccpnmr-2.5.2-linux-x86_64-standalone.tar.gz):

   tar -xzf ccpnmr-2.5.2-linux-x86_64-standalone.tar.gz
   cd ccpnmr-2.5.2-linux-x86_64-standalone

2. Run it (optionally pointing at an existing project directory):

   ./bin/analysis                 # or: ./bin/analysis /path/to/project

3. Non-GUI utilities (NEF import/export):

   ./runtime/bin/ccpnmr-nef import file.nef [--project-name NAME] [--force]
   ./runtime/bin/ccpnmr-nef export <project-directory> <output.nef>

Host requirements: a Linux x86_64 desktop with the usual X11 graphics libraries (libX11, libGL) — nothing else is read from or written to the system. The tree is relocatable: move it anywhere after unpacking.

The standalone tree is produced by ./make-standalone-linux.sh in the source repository (it rebuilds the wheel and packs it with the private runtime into dist/).

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NEF Project Files

CCPNMR Analysis reads and writes NEF v1.1 (BMRB Nmr_Exchange_Format) project files — metadata, molecules, chemical shifts, restraints and peak lists (never raw spectrum matrix data):

• GUI: Project → Export NEF… writes the current project to a .nef file (NEF is metadata + model, never raw spectrum matrix data — import is command-line only).
• Command line (standalone: ./runtime/bin/ccpnmr-nef; source / virtualenv installs: the ccpnmr-nef console command):

  ccpnmr-nef import file.nef [--project-name NAME] [--pdb PDB ...] [--force] [--relink [DIR]]
  ccpnmr-nef export <project-directory> <output.nef>