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locscale-surfer

https://github.com/cryotud/locscale-surfer

Science Score: 67.0%

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    Found 3 DOI reference(s) in README
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    Links to: zenodo.org
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    Scientific vocabulary similarity
    Low similarity (11.7%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Basic Info
  • Host: GitHub
  • Owner: cryoTUD
  • License: other
  • Language: Python
  • Default Branch: main
  • Size: 63.6 MB
Statistics
  • Stars: 1
  • Watchers: 1
  • Forks: 0
  • Open Issues: 0
  • Releases: 2
Created 11 months ago · Last pushed 9 months ago
Metadata Files
Readme License Citation

README.md

GitHub Release Python 3.11 License DOI

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: bash git clone https://github.com/cryoTUD/locscale-surfer.git Note the full path of the cloned repository. PATHTOREPO = path/to/locscale-surfer

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

  3. Install the bundle by running the following command: chimerax 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]
  • EMReady : 3-D SCUNet architecture. [GNU 3.0]

Owner

  • Name: AJ-Lab
  • Login: cryoTUD
  • Kind: user
  • Location: Delft en Provence
  • Company: Delft University of Technology

Citation (CITATION.cff) 

abstract: No description provided.
authors:
- affiliation: Delft University of Technology
  family-names: Alok Bharadwaj
  orcid: 0000-0002-7223-5648
- affiliation: Delft University of Technology
  family-names: Jakobi
  given-names: Arjen J.
  orcid: 0000-0002-7761-2027
cff-version: 1.2.0
date-released: '2025-05-22'
doi: 10.5281/zenodo.15488062
identifiers:
- type: swh
  value: swh:1:dir:122e7d2a0ee15e4461425d8dc83af6d83f1e860c;origin=https://doi.org/10.5281/zenodo.15488061;visit=swh:1:snp:060450b51fe0bf4ac0d6048cc7a20d4d86bd101a;anchor=swh:1:rel:ac4afa9d36a6e99519a88b122739bd55e0911b42;path=cryoTUD-locscale-surfer-b15246f
license:
- cc-by-4.0
message: If you use this software, please cite it as below.
repository-code: https://github.com/cryotud/locscale-surfer/tree/v0.1.0
title: LocScale-SURFER
type: software
version: v0.1.0

GitHub Events

Total
  • Release event: 2
  • Member event: 1
  • Push event: 61
  • Create event: 5
Last Year
  • Release event: 2
  • Member event: 1
  • Push event: 61
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Dependencies

docs/requirements.txt pypi
  • mkdocs-material *