Intel Mac OS X

Under Mac OS X, due to the free availability of XCode Tools which can be freely downloaded upon registration, we did not attempt to build Open3DALIGN with other tools. For BLAS and LAPACK functionality, we could not rely on the Accelerate Framework bundled in the XCode Tools since, as of Mac OS X 10.7, it is not thread-safe.

Therefore you will need to build and install the ATLAS libraries including full LAPACK functionality according to the instructions reported on the ATLAS website.
First, you will have to install Open3DQSAR and its dependencies as described in detail here. Afterwards, you simply need to move to the folder where you have downloaded open3dalign-X.Y.tar.gz, where X and Y are the major and minor version numbers, and build open3dalign:

$ tar -xzf open3dalign-X.Y.tar.gz
$ cd open3dalign-X.Y
$ ./bootstrap
$ ./configure CC=gcc-4.2 \
        CFLAGS="-Wall -O3 -msse3 -m64 \
        -I/build/include" \
        LDFLAGS="-L/build/lib64" \
        --with-atlas \
        --prefix=/build

Clearly, the paths reported in the example above might vary slightly according to your specific installations details.

Subsequently, type

$ make
$ make install

These commands will build Open3DALIGN for a 64-bit CPU with SSE3 extensions and install the open3dalign executable binary into /build/bin and documentation into /build/share/doc/Open3DALIGN. You might have to tweak the value of the CC variable according to the version of your XCode Tools.