LocScale-SURFER

ChimeraX Bundle

LocScale-SURFER is a ChimeraX bundle for enhancing visualisation and interpretation of LocScale2.0-optimised maps containing contextual structure.

It currently supports the detection and targeted segmentation/removal of micellar/membranous structures, but may be extended to other contextual structures in the future.

LocScale-SURFER runs on Linux, MacOS or Windows WSL platforms and is GPU-accelerated if GPU is available, but also runs on CPUs if required.

Documentation

Important

Please visit https://cryotud.github.io/locscale-surfer/ for comprehensive documentation, tutorials and troubleshooting.

Installation

From the ChimeraX toolshed:

toolshed install locscalesurfer

From source code:

1. Clone the repository:

git clone https://github.com/cryoTUD/locscale-surfer.git

Note the full path of the cloned repository. PATH_TO_REPO = path/to/locscale-surfer

2. Open ChimeraX and navigate to the command line interface.

3. Install the bundle by running the following command:

devel install PATH_TO_REPO
devel clean PATH_TO_REPO

4. Restart ChimeraX.
5. You should now see the LocScale-SURFER tool in: Tools > Volume Data > LocScale-SURFER

Credits

LoScale-SURFER is facilitated by a number of open-source projects.

• OPM database: Orientations of Proteins in Membranes (OPM) database.
• Optuna: Hyperparameter optimisation. [MIT license]
• SCUNet: Semantic segmentation. [Apache 2.0]