/ArtiaX

ArtiaX is an open-source extension of the molecular visualisation program ChimeraX.

Primary LanguagePythonGNU General Public License v3.0GPL-3.0

ArtiaX

for_readme

ArtiaX is an open-source extension of the molecular visualisation program ChimeraX and is primarily intended for visualization and processing of cryo electron tomography data. It allows easy import and export of particle lists in various formats and performant interaction with the data on screen and in virtual reality.

Features include:

  • Particle Picking
  • Particle orientation on screen and in VR
  • Isosurface visualization at particle locations
  • Interactive particle sub-setting based on metadata
  • Rendering particles using metadata-based colormaps

Read the companion paper on bioRxiv.

Install ArtiaX

Using the ChimeraX toolshed

  1. Download the latest Version of ChimeraX (version >= 1.3) to your operating system from here: ChimeraX Download.

  2. Run these commands in the ChimeraX shell:

toolshed reload available

toolshed install ArtiaX

  1. Relaunch ChimeraX

Using the wheel file

  1. Download the latest Version of ChimeraX (version >= 1.3) to your operating system from here: ChimeraX Download.

  2. Download the latest release.

  3. Open ChimeraX and install the package using the command:

toolshed install ChimeraX_ArtiaX-VERSION-py3-none-any.whl

  1. Relaunch ChimeraX.

References

  • ChimeraX:

    • UCSF ChimeraX: Structure visualization for researchers, educators, and developers. Pettersen EF, Goddard TD, Huang CC, Meng EC, Couch GS, Croll TI, Morris JH, Ferrin TE. Protein Sci. 2021 Jan;30(1):70-82.

    • UCSF ChimeraX: Meeting modern challenges in visualization and analysis. Goddard TD, Huang CC, Meng EC, Pettersen EF, Couch GS, Morris JH, Ferrin TE. Protein Sci. 2018 Jan;27(1):14-25.

  • Mycoplasma genitalium cell (left banner, rendered using ArtiaX)

    • Structural characterization of the NAP; the major adhesion complex of the human pathogen Mycoplasma genitalium. Scheffer MP, Gonzalez-Gonzalez L, Seybert A, Ratera M, Kunz M, Valpuesta JM, Fita I, Querol E, Piñol J, Martín-Benito J, Frangakis AS. Molecular Microbiology 2017, 105(6), 869–879.

  • HIV capsid locations (right banner, rendered using ArtiaX)

    • A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0. Zivanov J, Otón J, Ke Z, Qu K, Morado D, Castaño-Díez D, Kügelgen A Bharat TAM, Briggs JAG, Scheres SHW. BioRxiv 2022, 2022.02.28.482229. https://doi.org/10.1101/2022.02.28.482229

    • An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation. Schur FKM, Obr M, Hagen WJH, Wan W, Jakobi AJ, Kirkpatrick JM, Sachse C, Kräusslich HG, Briggs, JAG. Science 2016, 353(6298), 506–508.