See also: ChimeraX ToolshedMitoTNT
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).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.
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:
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.