US-align Universal Structure Alignment

You can install US-align using Homebrew or Conda. Note that these packages may not always contain the most recent version of the software.

• Homebrew (MacOS x86_64/arm64, Linux x86_64): Use brew install brewsci/bio/usalign.
• Conda (Linux x86_64/aarch64, MacOS x86_64/arm64): Use conda install -c bioconda usalign.

# Homebrew
brew install brewsci/bio/usalign

# Conda
conda install -c bioconda usalign

To perform a basic alignment between two structures, provide the file paths as arguments. US-align supports various formats including PDB, PDBx/mmCIF, and AlphaFold CIF.

To see a brief instruction set, run the program without arguments. To see the full list of available options, use the -h flag.

# Basic alignment usage
./USalign structure1.pdb structure2.pdb

# View help
./USalign -h

You can compile US-align from source on Linux, Mac OS, or Windows (via WSL2). The program requires g++ version 4.8.5 or later, clang++ version 12.0.5 or later, or mingw-w64 version 9.3 or later.

Linux/WSL2: Use make or compile directly with g++ using the -static flag for a static executable.

Mac OS: Do not use the -static flag, as Mac OS does not support building static executables.

Note on compressed files: On Linux and Mac OS, US-align can read .gz compressed files if the gunzip command is available in your environment. Native Windows builds (without WSL2) cannot parse .gz files due to lack of POSIX support.

# Using make
make

# Or direct compilation on Linux
g++ -static -O3 -ffast-math -lm -o USalign USalign.cpp