Compared to Chimera, ChimeraX has a more modern user interface, better graphics, and much faster handling of large structures. For more information, see:

• ChimeraX Advantages, Feature Highlights, User Guide, Tutorials, Change Log
• ChimeraX Presentations and Videos
• UCSF ChimeraX: Structure visualization for researchers, educators, and developers, Pettersen et al., Protein Sci. 30(1):70 (2021).

ChimeraX has several completely new features compared to Chimera (see advantages), but not yet all of its commonly used capabilities. Some features are implemented as commands only, not (yet) as graphical interfaces. Missing features include charge assignment and parametrization of nonstandard residues (except in the ISOLDE plugin), dock prep, saving and restoring scenes, animation GUI, 2D label GUI, render by attribute GUI, “worms” to show residue attributes, trajectory analysis other than simple playback, calculating a multiple sequence alignment from a multiple structure superposition, and many others. Chimera capabilities grew significantly over several years, and likewise, ChimeraX will contain more of these important features as development proceeds.

Although similar in many aspects, ChimeraX is not backward compatible with Chimera and does not read Chimera session files. Chimera includes an export to ChimeraX feature that covers some but not all types of data.