Per-model clipping in ChimeraX is done with the clip command, or with the clipping mouse modes, atom radii are set with the size command, visibility is set with the show/hide commands, color is set with the color command, there are volume tracer mouse modes, and saving marker files should work, although you hit some bug and should press the Report a Bug… button when you get that traceback. ChimeraX does not have the selection inspector window yet. ChimeraX uses a different window toolkit Qt while Chimera used Tk so it requires all new code to move any graphical user interface from Chimera to ChimeraX. ChimeraX is a completely new program, modernizing every component of the 20-year-old design of Chimera so even moving commands from Chimera to ChimeraX requires substantial work.

If you don’t find ChimeraX ready for your use, of course you should continue to use Chimera. We expect ChimeraX to replace Chimera in a few years. You might want to spend an hour skimming Elaine’s thorough ChimeraX documentation to understand what is in ChimeraX, including many new features like virtual reality that are not in Chimera.

On Feb 26, 2019, at 2:03 AM, Jun Ha Song wrote:

Tom,

I recently got HTC Vive, and therefore started using ChimeraX. I have to say; the VR functionality is amazing. The ability to VR alone is sufficient reason for me to move over to ChimeraX.

However, I noticed that key, crucial, irreplaceable features are (as far as I am aware) non-existent on ChimeraX. Below are function/tools that exist in Chimera that I use (literally) everyday, and I am wondering if these function/tools can also be implemented on ChimeraX or not.

- per-model clipping (mclip)
- inspect selection (ability to change atom/bond/surface radius, visibility, color)
- volume tracer (ability to save markerset or atom/bond as .cmm)

If the circumstance is so that implementing these onto ChimeraX is not feasible, then I must remain with Chimera until similar tools become available on ChimeraX.

Also, is there any particular reason why all the tools of Chimera are not copied onto ChimeraX? Is ChimeraX trying to be another program that is different from Chimera?

As for "ability to save .cmm", I tried saving atom/link using command

save E:\LBNL\Stereocilia\ChimeraX_Markerset.cmm format markers models #1

but I got error saying that

NotImplementedError: Slices are not implemented.
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\markers\cmmfiles.py", line 39, in markerset_as_xml
rgb = tuple(r/255 for r in m.color[:3])
See log for complete Python traceback.

is this a simple bug during development, or have I typed wrong command?

Best,
Junha Song.