ChimeraX-Related Software ChimeraX home icon

See also: ChimeraX Toolshed

AutoEMage
AutoEMage automates cryo-electron (cryo-EM) microscopy file transfer, motion correction, CTF estimation, image display, outlier detection, particle picking, 2D classification, class ranking, and model generation. It uses MotionCor2, CTFFIND4, UCSF ChimeraX, RELION, and IMOD, and is described in Cheng et al., J Appl Cryst 56:1865 (2023).
ContinuousFlex
ContinuousFlex is a plugin to Scipion for continuous conformational flexibility analysis of cryo-EM data. It uses ChimeraX for fitting and visualization, as described in Vuillemot et al., Int J Mol Sci 25:20 (2023).
MitoTNT
MitoTNT builds on MitoGraph segmentation and ChimeraX visualization for the analysis of mitochondrial networks in 4D live-cell fluorescence microscopy data, as described in Wang et al., PLoS Comput Biol:e101160 (2023).
MorphOT
MorphOT morphs density maps using shape interpolation based on optimal transport, as described in Ecoffet et al., Bioinformatics:btaa1019 (2020).
PTM-Psi
PTM-Psi is a Python package that includes a ChimeraX plugin to replace amino acid sidechains with certain post-translationally modified (PTM) forms, as described in Mejia-Rodriquez et al., Protein Sci:e4822 (2023). The initial library includes several common cysteine PTMs, and a broader range of types may be offered in the future.
pyCapsid
pyCapsid is a Python package to extract quasi-rigid domains in protein shells and other macromolecular complexes, with output including a script for ChimeraX visualization. It is available as a Google Colab notebook and as code on Github for those who wish to install it locally. See the online tutorial and Brown et al., Bioinformatics 40:btad761 (2024).
pyLattice
pyLattice is a library of Python modules, Jupyter notebooks, and Matlab routines that operate together to form an image analysis pipeline for lattice light-sheet microscopy, as described in Schöneberg et al., Mol Biol Cell 29:2959 (2018). It provides customized input for 4D (3D + time) visualization in ChimeraX.
relionsubtomo2ChimeraX
Python script to convert Relion star file into ChimeraX visualization command script.
RNArtist
RNArtist allows designing RNA 2D structures interactively and using UCSF ChimeraX (or UCSF Chimera) to explore 3D architectures. RNArtist is developed by Fabrice Jossinet at the Institut de Biologie Moléculaire et Cellulaire, Strasbourg.

ScanNet Server
The ScanNet server predicts protein-binding sites for structures in the PDB, the AlphaFold Database, or uploaded from a local file. The method is described in Tubiana et al., Nat Methods 19:730 (2022) and the web server specifically in Tubiana et al., J Mol Biol 434:167758 (2022). Results are emailed to the user as a zip file containing:
  • the PDB file with binding site probabilities in the B-factor field
  • csv file containing the binding site probabilities
  • ChimeraX command script (.cxc) for visualizing the results (right-click → open the file with ChimeraX)
  • Chimera python script (.py) for visualizing the results (right-click → open the file with Chimera)

SymProFold
SymProFold combines AlphaFold-Multimer predictions with general symmetry considerations to predict symmetric protein assemblies such as bacterial S-layers and viral capsids. It creates an mmCIF file containing the primitive unit cell and symmetry information of the predicted assembly. The related tool Domain_Separator separates an atomic structure into structural domains. Both tools use ChimeraX methods and libraries and are described in Buhlheller et al. (preprint 2023, DOI: 10.21203/rs.3.rs-3830312/v1).

xiView
xiView is a web-based visualisation tool for the analysis of cross-linking mass spectrometry results, as described in Graham et al., bioRxiv (2019). 3D export options include UCSF ChimeraX pseudobond files.