Installing LocScale 2.0

System Compatibility

LocScale should run on any CPU system with Linux, OS X or Windows subsytem for Linux (WSL).

GPU: To run the feature_enhance option LocScale requires the availability of a GPU. It is possible to run it on CPUs but computation will be slow(er).
OpenMPI: LocScale allows parallelisation on multi-CPU environment with OpenMPI. If no OpenMPI environment exists, joblib is used for parallelisation.

Installation on Apple silicon

GPU support on Apple silicon (MX chip) has now been fixed and should work seamlessly.

We recommend to use Conda for a local working environment. See here for more information on what Conda flavour may be the right choice for you, and here for Conda installation instructions.

Quick installation

Install LocScale 2.0 and get up and running in minutes.

Set up in 5 min
Step-by-step instructions

Step-by-step installation installation instructions.

Install guide

Installation via environment files:

1. Install REFMAC5 via CCP4/CCPEM

LocScale needs a working instance of REFMAC5. If you already have CCP4/CCPEM installed check if the path to run refmac5 is present in your environment.

which refmac5

If no valid path is returned, please install CCP4 to ensure refmac5 is accessible to the program.

2. Install LocScale using environment files

You will see environment.yml file in the main repo. Download this file to your local computer.

Once you download the yml file:

conda env create -f /path/to/environment.yml
conda activate locscale2

Installation using PyPi (pip)

You can also follow these steps to install locscale using pip.

1. Create and activate a new conda environment

conda create -n locscale python=3.11
conda activate locscale

2. Install fortran compiler

LocScale uses Fortran code to perform symmetry operations and requires a Fortran compiler to be present in your system. You can install gfortran from conda-forge.

conda install -c conda-forge gfortran

3. Install REFMAC5 via CCP4/CCPEM

The model-based and hybrid map sharpening modes of LocScale need a working instance of REFMAC5. If you already have CCP4/CCPEM installed check if the path to run refmac5 is present in your environment. For model-free sharpening and confidence-aware density modification REFMAC5 is not required.

which refmac5

If no valid path is returned, please install CCP4 to ensure REFMAC5 is accessible.

4. Install LocScale and dependencies using pip

Recommended installationDevelopment versionEditable mode

We recommend using pip for installation. Use pip version 21.3 or later to ensure all packages and their version requirements are met.

pip install locscale

Install development version

If you would like to install the latest development version of locscale, use the following command to install from the git repository.

pip install git+https://github.com/cryoTUD/locscale.git

To install the git repository in editable mode, clone the repository, navigate to the locscale directory, and run pip install -e.

5. Testing

To test functionality after installation, you can run LocScale unit tests using the following command:

locscale test