id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
19227	Survey of Claude AI problems controlling ChimeraX	Tom Goddard	Tom Goddard	"The purpose of this ticket is to document the many problems that prevent Claude from successfully controlling ChimeraX, and use this list to figure out how best to improve Claude's capabilities with ChimeraX.

I've used Claude to control ChimeraX through MCP (Model Context Protocol) for about 5 hours on real-world easy-to-hard difficult biology  problems that ChimeraX can handle.  I'd estimate Claude runs into some problem about 20 times per hour, and I have encountered dozens of different failure modes.

Since there are so many problems I'll number them so it is easy to add comments refering to specific issues.  Some of the problems are very general (e.g. Claude hits maximum conversation size limit) and some are narrow and techical (e.g. Claude gets model spec ranges wrong #1.1-1.5 instead of #1.1-5).  The general ones are fewer and I think more interesting in terms of improving the utility of Claude controlling ChimeraX so I'll put a ""G"" in the number for those issues to highlight those."	task	assigned	moderate		UI				Zach Pearson Eric Pettersen a.rohou@… iamkaant@…				all	ChimeraX