You can get ISOLDE from its repo at https://github.com/tristanic/isolde Then edit the pyproject.toml so that the dependency on ChimeraX-Core is compatible with prerelease dev versions, something like ChimeraX-Core~=1.11dev (I consider tilde equals harmful, but we’re stuck with it). IIRC Tristan usually waits until pretty late in the release cycle to prepare ISOLDE for the next ChimeraX, so YMMV -- Zach
On 21 Oct 2025, at 08:41, Alexis Rohou <a.rohou@gmail.com> wrote:
Thanks Zach!
You had the right intuition - this was not a first build. I had done a git pull and then make install. I followed your instructions, removed the ChimeraX.app folder and did `make build-from-scratch` and everything worked fine.
Perhaps this is a question for Tristan, but is there a way to build a compatible version of ISOLDE?
Cheers, Alexis
On Mon, Oct 20, 2025 at 11:01 PM Zach Pearson <z.pearson9@gmail.com> wrote: Hi Alexis,
Was this from your first build, or a second build? Sometimes I encounter this error if I’m building a bundle for a second time without a make clean in between, so I always rm -r ChimeraX.app and use the build-from-scratch make target.
— Zach
On 20 Oct 2025, at 19:40, Alexis Rohou via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello,
I'd like to build from source in order to play with (and possibly hack at) the MCP server.
I am on macOS 14.7.6 with Xcode 16.2.
I think the compilation went well, but at link time I get warnings and an error. Below is the end of the output of `make install`. What do you recommend I try?
Cheers, Alexis
available bundle cache has not been initialized yet Executing: devel install . user false exit true noDeps true ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/pyinstance_cpp/PythonInstance.o) was built for newer 'macOS' version (11.0) than being linked (10.9) ld: warning: object file (/Users/rohoua/work/git/ChimeraX/src/bundles/atomic_lib/atomic_cpp/element_cpp/Element.o) was built for newer 'macOS' version (11.0) than being linked (10.9) ar: src/lib/libatomstruct_tmpl.a is a fat file (use libtool(1) or lipo(1) and ar(1) on it) ar: src/lib/libatomstruct_tmpl.a: Inappropriate file type or format Traceback (most recent call last): File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/setuptools/_distutils/spawn.py", line 87, in spawn subprocess.check_call(cmd, env=_inject_macos_ver(env)) File "/Users/rohoua/work/git/ChimeraX/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/subprocess.py", line 413, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/usr/bin/xcrun', 'ar', 'rcs', 'src/lib/libatomstruct_tmpl.a', 'atomic_cpp/atomstruct_cpp/tmpl/Atom.o', 'atomic_cpp/atomstruct_cpp/tmpl/Bond.o', 'atomic_cpp/atomstruct_cpp/tmpl/CoordSet.o', 'atomic_cpp/atomstruct_cpp/tmpl/Molecule.o', 'atomic_cpp/atomstruct_cpp/tmpl/Residue.o', 'atomic_cpp/atomstruct_cpp/tmpl/TemplateCache.o', 'atomic_cpp/atomstruct_cpp/tmpl/amino.o', 'atomic_cpp/atomstruct_cpp/tmpl/camino.o', 'atomic_cpp/atomstruct_cpp/tmpl/findres.o', 'atomic_cpp/atomstruct_cpp/tmpl/general.o', 'atomic_cpp/atomstruct_cpp/tmpl/ions.o', 'atomic_cpp/atomstruct_cpp/tmpl/namino.o', 'atomic_cpp/atomstruct_cpp/tmpl/nucleic.o']' returned non-zero exit status 1. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/