Thank you, Alexis. I have no experience in building ChimeraX myself, so I will wait for the daily build with your changes.

 -- Andrii

On 10/27/25 4:10 PM, Alexis Rohou wrote:
Hi Andrii,

I didn't really investigate Claude Skills. I'm sticking to MCP for now, since it seems to be mostly working for me. 

Your problems 2-4 sound exactly like what I was having trouble with until Friday afternoon. But the work I did over the week-end I believe (mostly) solves them. If you can build from source, you could build my fork of the project and I'd be curious to see whether the problems you encountered are still there (if so, could you share the exact prompts you tried so we can add them to the suite of test prompts?). If not, perhaps wait until the team's had a chance to review my pull request and then you can try again with a new daily build. 

Cheers,
Alexis

On Mon, Oct 27, 2025 at 2:59 PM Andrii Kyrylchuk via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi Everyone,

Thank you for the tool, Alexis! Great work!

  1. I created a Claude Skill based on the MCP based on the idea from this Reddit post. The OP’s script didn’t work for me, so I used Claude to create all the files needed for the Skill. It seems to work fine, and should save context, but I’m new to Skills and don’t know how to check. I can share the files if anyone is interested. I think Skills are supposed to be the extension of MCP.

  2. I’ve also had maximum conversation length error several times. In some cases, the complexity of the chat structure overwhelmed the Claude window and the chat screen turned blank. This is also the case for the web-version.

  3. One particular example that Claude seems to struggle with is focusing the view on a single ligand molecule if several copies of a ligand are present. In my tests, Claude tried 30 different commands but couldn’t get it.

  4. When asked to “show” or “display” something, Claude is eager to capture a screenshot of the final state and then pour it into the chat, which leads to the maximum conversation length error. I think a custom instruction (or a part of the Skill) preventing this would be useful.

Sincerely,
Andrii

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