A couple of minor corrections below on the tool names (sorry about that!)... Best, Elaine

On May 4, 2023, at 10:51 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Fabrizio Fierro, Please see the commercial licensing page, which has a section entitled "ChimeraX vs. Chimera" as well as instructions on going forward if you decide to pursue a license:

<https://www.rbvi.ucsf.edu/chimera/commercial_license.html>

I encourage viewing the above, as it tries to give the picture as well as link to lists of specific advantages of ChimeraX over Chimera, and specific features that were in Chimera but not yet in ChimeraX. I also include a couple of these links here:

<https://www.rbvi.ucsf.edu/chimerax/docs/user/advantages.html> <https://www.rbvi.ucsf.edu/chimerax/progress.html>

Near the top of the commercial licensing page, it also mentions that we do not offer free trials, sorry.

To answer more specifically about cryoEM functionality, that is an area we have focused on intensively. Thus, ChimeraX contains substantially all of the map-related functionality of Chimera, and goes beyond it with advanced capabilities including the ISOLDE flexible flitting plugin. So my short answer to your question #2 is yes. Still, there are differences in the interface and how the features are accessed, and not an exact 100% overlap of every detailed option, so I encourage you to think about your workflow and make sure what you need is there.

ChimeraX User Guide: <https://www.rbvi.ucsf.edu/chimerax/docs/user/index.html>

I'll try to list major relevant features here, but do feel free to write back if you have specific features you want to ask about.

ChimeraX includes the following, see the User Guide index for specific links for each tool and command: =-=-= Volume Viewer tool; although there are fewer settings in this GUI than Chimera, they are available via "volume" command

Atomic-structure building: de novo building of peptides and other types of molecules, and Modeller interface (and AlphaFold and ESMFold tools, which were not in Chimera)

Segment Map

Fitting into maps: Fit in Map and Fit to Segments (similar to in Chimera), ISOLDE plugin for flexible fitting with interactive dynamics and many additional building features, available from ChimeraX Toolshed (goes far beyond what was available in Chimera)

Volume Eraser

in ChimeraX this is the Map Eraser tool

Map Tracer (like Chimera's Volume Tracer)

in ChimeraX this is Marker Placement tool

Map Statistics

Color Zone

Other map processing: "volume" subcommands (like vop command in Chimera)

We are also working on integration of ChimeraX with some parts of the Phenix software. =-=-=

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On May 4, 2023, at 6:12 AM, Fabrizio Fierro via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi,

I work for a startup called Protai and I am interested in ChimeraX.

1) Are all the functions available in Chimera implemented also in ChimeraX? 2) Specifically, with Chimera it was easy to load, visualize and work with cryoEM maps. Does ChimeraX work in the same way? 3) Would it be possible to get a free trial period for ChimeraX?

Thanks,

Fabrizio Fierro.

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