I think you are talking about differences between Chimera and ChimeraX.  Those are two different programs.  That is why features and command syntax differ.

  Here is a bit of history if you are interested.  Chimera was developed from 1995 to 2015 and ChimeraX from 2015 to the present, both developed by the UCSF Computer Graphics Lab.  We decided in 2015 that it was not sensible to continue Chimera development because it was based on 20-year old technologies, the Tk window toolkit and Python 2, and old OpenGL from before GPU shaders.  So we opted to start a new program called ChimeraX based on the Qt window toolkit, Python 3 and modern OpenGL.  Chimera was created over 20 years with 5 UCSF developers, and it was not feasible to reproduce that 100 person years of Chimera development in the new ChimeraX.  Also we wanted to improve things that were not done well in Chimera for instance the way chains were specified in commands.  Making a new program gave us an opportunity to fix things that could not be backward compatible.  The result is that in the last 10 years ChimeraX has most of the useful old Chimera features but not all of them.  And ChimeraX has many new advances such as AlphaFold, Boltz, and OpenFold structure prediction and dozens of other new capabilities that Chimera did not have.  The UCSF Computer Graphics Lab has existed since the 1970s and made earlier molecular graphics programs.  Before Chimera there was MidasPlus, before MidaPlus there was Midas.  Before Midas I think there was one called MIDS.  Each of these programs had a long life and then was replaced with a new program that kept the good features of the older program, added many new features, and broke compatibility to fix mistakes learned from a decade or more of use of the previous program.

  If there are specific features from Chimera that are not in ChimeraX that you like tell us on the mailing list.  I'm not sure what you mean by the function "icosahedral"?  There was an Icosahedral Cage GUI in Chimera and a "shape icosahedron" command and a related hkcage command.  The Icosahedral Cage GUI is not in ChimeraX, the commands are in ChimeraX.  I developed those Chimera capabilities.  I liked the Icosahedral Cage GUI, but other capabilities such has machine learning structure prediction have had priority being more valuable to more people and I have not had time to recreate Isosahedral Cage in ChimeraX.  We welcome outside developers making plugins for ChimeraX (https://cxtoolshed.rbvi.ucsf.edu/) and an Icosahedral Cage GUI would be easy for someone to contribute if they had the time and desire.

Tom