frangakislab/artiax

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

ArtiaX

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

3. 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

4. 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.

artiax's Issues

artiax colormap command cannot be used

Hi, thanks for the amazing work putting these visualisation plugins to work. Really splendid work!

I just have a little issue with the command 'artiax colormap' when I tried to color my particles based on the star file metadata imported from RELION. For example, if I want to color the particles using 'rlnMaxValueProbDistribution', I can do so with the interactive GUI you provided.
But when I typed the same command -

'artiax colormap #1.2.1.3 rlnMaxValueProbDistribution palette redgreen minValue 0.015419 maxValue 0.982082 transparency 0.0'

and tried it again in ChimeraX, it returned me with an error saying

'artiax colormap: Model #1.2.1.3 - "Markers" is not a particle list model.'

I am pretty sure the command is the same as what's been executed by the interactive GUI as reflected from the log information. Do you know anything about this issue? Please advise. Thanks!

P.S. the purpose for me trying to execute the command manually is to change the color palette to something else, because at the moment, there is only one option redgreen to chose from.

Support for STOPGAP motivelists in STAR format

First of all, thanks a lot for this really useful ChimeraX plugin!

I've added support for reading STOPGAP v0.7.1 (https://github.com/williamnwan/STOPGAP) motivelists in STAR format:

rdrighetto@eb6d353

Known issues:

• Currently only works if "STOPGAP star files" is explicitly selected as the file type in the "Open File..." dialog for particle lists. Otherwise, it tries to open it as a RELION .star format, since both use the same extension (and strictly speaking it's the same STAR file format, but obviously the fields are different for each package). Would be nice to resolve this ambiguity in a more elegant and automated way.

• Writing as STOPGAP .star motivelist currently not supported, for two reasons:
  -- One is that I was not able yet to correct the coordinates offset by 1 voxel as in the Artiatomi motivelist format i.e. .em/.av3 format), when writing;
  -- Second, the starfile module is currently writing out a RELION .star file header and I don't know how to change that.
  Help implementing write_file() in STOPGAPParticleData.py would be very much appreciated!

I would be happy to make a pull request if the ArtiaX developers agree, please let me know if you have any questions.

Best wishes,
Ricardo

Rotate Selected not working in ChimeraX 1.7

In ChimeraX 1.6/ArtiaX 0.3, when "Rotate Selected" was active, dragging with the right mouse button near the centre of the screen rotated the particle around the x and y axes of the user view and dragging with the right mouse button at the edge of the screen rotated the particle around the z axis of the user view. In ChimeraX 1.7/ArtiaX 0.3 even if I drag at the very edge of the view I can only rotate in x and y. This makes it very difficult to correctly orient particle axes in the tomogram plane.

Dragging at the edge of the screen still rotates around z when the normal ChimeraX Right Mouse/Rotate Model is active, so I think this is an ArtiaX-specific issue.

For now I have gone back to ChimeraX 1.6

feature request: opening particles from single tomogram

Hi,

ArtiaX is really nice, but there are two things that seem (hopefully) easy enough to implement that would massively help the user experience. First, and most importantly, being able to display only the particles from one tomogram (with eg. the tomo ID in rlnMicrographName) when opening a star file.

Second, the ability to add custom color palettes would be very very nice.

If possible, it would be awesome to see these things (or at least #1) implemented :)

Thanks for the great software.

Doesn't work correctly with Dynamo table

When I tried to use ArtiaX with dynamo, it didn't display the particle orientation properly. With the same dataset, converting to Relion4 format, then ArtiaX displayed the star file correctly. Can you check this?

Missing sections in STAR file

Hi, I used ArtiaX to clean my subtomograms based on their orientation, but some sections are missing when I save a new data set as STAR file. These 3 positions are gone: _rlnImageName _rlnCtfImage _rlnMicrographName. Because of that, I can no longer use it in RELION. Is there any way of fixing it? Thank you!

Closing the main ArtiaX model causes tool to crash.

As reported here.

ArtiaX models cannot be saved in ChimeraX sessions.

At the moment, saving in ChimeraX sessions causes errors, as reported here.

Saved Particle Lists are written in angstroms and not pixels

Importing a Particle List created in 3dmod (.mod) is displayed correctly on the tomogram file loaded into ArtiaX. However, when saving the Particle List as a new .mod file, the coordinates are scaled by the Angstrom/pixel value. This was confirmed by comparing the coordinates written by IMOD's model2point on the .mod file generated by 3dmod and the saved .mod file from ArtiaX:

$ model2point 3dmod.mod model2point_3dmod.coords
$ head -n 1 model2point_3dmod.coords
551.33 966.00 317.00

$ model2point ArtiaX.mod model2point_ArtiaX.coords
$ head -n 1 model2point_chmx.coords
4774.55 8365.56 2745.22

For this data, there is 8.66 Angstroms/pixel.