id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20573 Boltz fails with numpy 2.4 due to numba requiring numpy version <= 2.1 goddard@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.5.2-arm64-arm-64bit ChimeraX Version: 1.13.dev202606302219 (2026-06-30 22:19:15 UTC) Description Boltz structure prediction fails with numpy 2. Boltz reports that numba requires numpy 2.1 or less while ChimeraX is providing numpy 2.4. Log: UCSF ChimeraX version: 1.13.dev202606302219 (2026-06-30) © 2016-2026 Regents of the University of California. All rights reserved. > open /Users/goddard/Desktop/test.cxs format session Log from Wed Jul 1 15:28:34 2026UCSF ChimeraX version: 1.13.dev202606302219 (2026-06-30) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 8ef5 format mmcif fromDatabase pdb 8ef5 title: Fentanyl-bound mu-opioid receptor-Gi complex [more info...] Chain information for 8ef5 #1 --- Chain | Description | UniProt A F | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340 C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_BOVIN 1-68 E | scFv16 | M R | Mu-type opioid receptor | OPRM_HUMAN 2-368 Non-standard residues in 8ef5 #1 --- 7V7 — N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide CLR — cholesterol > ui tool show ""Render/Select by Attribute"" > color byattribute a:bfactor #!1 target absc palette > 63.64,blue:98.675,white:133.71,red 11705 atoms, 1453 residues, atom bfactor range 63.6 to 134 > close > open 1a0m 1a0m title: 1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...] Chain information for 1a0m #1 --- Chain | Description | UniProt A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16 Non-standard residues in 1a0m #1 --- NH2 — amino group 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > ui tool show ""Crystal Contacts"" > crystalcontacts #1 10 pairs of asymmetric units of 1a0m contact at distance 3.0 A Atoms MTRIX SMTRY Unit cell MTRIXref Copies 16 0 5 0 0 0 0 1 16 0 5 0 0 -1 0 1 8 0 7 0 0 0 0 1 6 0 6 0 -1 -1 0 1 6 0 2 0 0 0 0 1 4 0 7 0 0 -1 0 1 4 0 6 0 -1 0 0 1 4 0 3 0 0 0 0 1 4 0 2 1 0 0 0 1 3 0 3 0 1 0 0 1 > close > open 9sgj coordsets true Summary of feedback from opening 9sgj fetched from pdb --- note | Fetching compressed mmCIF 9sgj from https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/sg/pdb_00009sgj/structures/pdb_00009sgj.cif.gz 9sgj title: Fd3 tentative ancient version of modern ferodoxin fold [more info...] Chain information for 9sgj #1 --- Chain | Description A | Fd3 9sgj has 30 coordinate sets > md cluster #!1 start 1 step 1 end 30 > close > open 1a0m 1a0m title: 1.1 angstrom crystal structure of A-conotoxin [TYR15]-epi [more info...] Chain information for 1a0m #1 --- Chain | Description | UniProt A B | ALPHA-CONOTOXIN [TYR15]-EPI | CXA1_CONEP 1-16 Non-standard residues in 1a0m #1 --- NH2 — amino group 8 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > usage swapaa swapaa residues resTypes [angleSlop a number] [bfactor a number] [criteria criteria] [density a density map specifier] [distSlop a number] [hbondAllowance a number] [ignoreOtherModels true or false] [rotLib rotLib] [log true or false] [preserve preserve] [relax true or false] [retain true or false] [scoreMethod scoreMethod] [overlapCutoff a number] — Swap amino acid side chain(s) resTypes: some text strings criteria: some an integer ≥ 0 or a text string rotLib: one of Dunbrack, Dynameomics, Richardson.common, or Richardson.mode preserve: a number ≥ 0 scoreMethod: one of num or sum swapaa interactive residues resTypes [rotLib rotLib] [log true or false] — Show possible side-chain rotamers resTypes: some text strings rotLib: one of Dunbrack, Dynameomics, Richardson.common, or Richardson.mode swapaa mousemode residues restypes — Replace residue with specified amino acid restypes: a collection of one of ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, or VAL > show atoms > swapaa /A:9 HIS Using Dunbrack library /A ASN 9: phi -57.7, psi -50.2 trans Applying HIS rotamer (chi angles: -179.8 96.8) to /A HIS 9 > ui mousemode right swapaa > swapaa mousemode /A:9 MET > close > open 8ef5 format mmcif fromDatabase pdb 8ef5 title: Fentanyl-bound mu-opioid receptor-Gi complex [more info...] Chain information for 8ef5 #1 --- Chain | Description | UniProt A F | Guanine nucleotide-binding protein G(i) subunit alpha-1 | GNAI1_HUMAN 1-354 B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | GBB1_RAT 2-340 C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | GBG2_BOVIN 1-68 E | scFv16 | M R | Mu-type opioid receptor | OPRM_HUMAN 2-368 Non-standard residues in 8ef5 #1 --- 7V7 — N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide CLR — cholesterol > usage findclash ""findclash"" is not a command name > style stick Changed 11705 atom styles > ui tool show Clashes > clashes sel restrict #1 overlapCutoff 0.0 ignoreHiddenModels true select > true No atoms match given atom specifier > ui tool show Clashes > select /R 2474 atoms, 2551 bonds, 293 residues, 1 model selected > clashes sel restrict #1 overlapCutoff 0.0 ignoreHiddenModels true select > true 253 clashes > ui tool show Scenes > scenes save """" > hide sel atoms > select clear > show cartoons > hide atoms > scenes save """" > scenes restore 1 > scenes restore 2 > show surfaces > scenes save """" > scenes restore 1 > scenes restore 2 > scenes restore 3 > save test.cxs ——— End of log from Wed Jul 1 15:28:34 2026 ——— > view name session-start opened ChimeraX session > scenes restore 2 > scenes restore 1 > scenes restore 2 > scenes restore 3 > hide #!1 models > ui tool show ""Cage Builder"" > view > close > open 9sgj format mmcif fromDatabase pdb coordsets true 9sgj title: Fd3 tentative ancient version of modern ferodoxin fold [more info...] Chain information for 9sgj #1 --- Chain | Description A | Fd3 9sgj has 30 coordinate sets > ui tool show OpenFold > openfold predict protein /A name 9sgj Running OpenFold prediction of protein with 75 residues on gpu Using multiple sequence alignment server https://api.colabfold.com Confidence pTM 0.61, , pLDDT 71 OpenFold prediction completed in 67 seconds (start openfold 12 sec, initialize neural net 29 sec, sequence search 0 sec, structure inference 17 sec) Please cite OpenFold-1 Democratizing Biomolecular Interaction Modeling. BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these predictions. > open > /Users/goddard/Desktop/openfold/9sgj/9sgj/seed_42/9sgj_seed_42_sample_1_model.cif > logInfo false Matchmaker 9sgj, chain A (#1) with 9sgj_seed_42_sample_1_model.cif, chain A (#2), sequence alignment score = 344 RMSD between 66 pruned atom pairs is 0.704 angstroms; (across all 75 pairs: 3.037) > ui tool show Boltz > boltz predict protein #1/A name 9sgj Running Boltz prediction of protein with 75 residues on gpu Using multiple sequence alignment server https://api.colabfold.com Running boltz prediction failed with exit code 1: command: /Users/goddard/boltz22/bin/boltz predict /Users/goddard/Desktop/boltz/boltz_9sgj/9sgj.yaml --use_msa_server --accelerator gpu --no_kernels stdout: stderr: /Users/goddard/boltz22/lib/python3.11/site- packages/torchmetrics/__init__.py:31: UserWarning: A NumPy version >=1.22.4 and <2.3.0 is required for this version of SciPy (detected version 2.4.6) import scipy.signal Traceback (most recent call last): File ""/Users/goddard/boltz22/bin/boltz"", line 5, in from boltz.main import cli File ""/Users/goddard/boltz22/lib/python3.11/site-packages/boltz/main.py"", line 23, in from boltz.data.module.inference import BoltzInferenceDataModule File ""/Users/goddard/boltz22/lib/python3.11/site- packages/boltz/data/module/inference.py"", line 11, in from boltz.data.feature.featurizer import BoltzFeaturizer File ""/Users/goddard/boltz22/lib/python3.11/site- packages/boltz/data/feature/featurizer.py"", line 5, in import numba File ""/Users/goddard/boltz22/lib/python3.11/site-packages/numba/__init__.py"", line 59, in _ensure_critical_deps() File ""/Users/goddard/boltz22/lib/python3.11/site-packages/numba/__init__.py"", line 45, in _ensure_critical_deps raise ImportError(msg) ImportError: Numba needs NumPy 2.1 or less. Got NumPy 2.4. OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 Ultra OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.11.0, Qt 6.11.0 Qt runtime version: 6.11.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac14,14 Model Number: Z1800003VLL/A Chip: Apple M2 Ultra Total Number of Cores: 24 (16 Performance and 8 Efficiency) Memory: 64 GB System Firmware Version: 18000.121.3 OS Loader Version: 18000.121.3 Software: System Software Overview: System Version: macOS 26.5.2 (25F84) Kernel Version: Darwin 25.5.0 Time since boot: 1 day, 22 hours, 59 minutes Graphics/Displays: Apple M2 Ultra: Chipset Model: Apple M2 Ultra Type: GPU Bus: Built-In Total Number of Cores: 60 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: PHL 278B1: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Installed Packages: 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Sphinx: 9.0.4 sphinx-autodoc-typehints: 3.6.1 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.4.5 stack-data: 0.6.3 starlette: 1.3.1 superqt: 0.7.6 tables: 3.11.1 threadpoolctl: 3.6.0 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.7 traitlets: 5.15.1 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.7.0 uvicorn: 0.49.0 wcwidth: 0.8.2 webcolors: 24.11.1 wheel: 0.47.0 wheel-filename: 1.4.2 yarl: 1.24.2 }}} " defect assigned normal Structure Prediction all ChimeraX