ChimeraX-Related Software

See also: ChimeraX Toolshed

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 morphs density maps using shape interpolation based on optimal transport, as described in Ecoffet et al., Bioinformatics:btaa1019 (2020).

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.

Python script to convert Relion star file into ChimeraX visualization command script.

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)

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.