#10242 closed defect (limitation)
Wrong version of regex installed
Reported by: | Owned by: | Tom Goddard | |
---|---|---|---|
Priority: | normal | Milestone: | |
Component: | Tool Shed | Version: | |
Keywords: | Cc: | chimera-programmers, Greg Couch, Tony Schaefer | |
Blocked By: | Blocking: | ||
Notify when closed: | Platform: | all | |
Project: | ChimeraX |
Description
The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description (Describe the actions that caused this problem to occur here) Log: > setattr a radius 1 Assigning radius attribute to 0 items UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/andrea/Desktop/scratch/xtbopt.xyz opened xtbopt.xyz as an XYZ coordinate file movie > close > open /Users/andrea/Desktop/scratch/xtbopt.xyz opened xtbopt.xyz as an XYZ coordinate file movie > close > open /Users/andrea/Desktop/scratch/xtbopt.xyz format xyz opened xtbopt.xyz as an XYZ coordinate file movie > close > open /Users/andrea/Desktop/scratch/ref.1_enam.out format out Summary of feedback from opening /Users/andrea/Desktop/scratch/ref.1_enam.out --- note | ref.1_enam.out has 0 imaginary harmonic vibrational modes Opened ref.1_enam.out as an ORCA output file > close > open /Users/andrea/Desktop/scratch/ref.1_enam.out format out Summary of feedback from opening /Users/andrea/Desktop/scratch/ref.1_enam.out --- note | ref.1_enam.out has 0 imaginary harmonic vibrational modes Opened ref.1_enam.out as an ORCA output file > ui tool show "Orbital Viewer" > open /Users/andrea/Desktop/scratch/orca_iodo.out Summary of feedback from opening /Users/andrea/Desktop/scratch/orca_iodo.out --- note | orca_iodo.out has 0 imaginary harmonic vibrational modes Opened orca_iodo.out as an ORCA output file Opened MO alpha 91 as #2.1, grid size 110,91,71, pixel 0.151,0.151,0.151, shown at level -0.061,0.061, step 1, values float64 > hide #!2 models Opened MO alpha 194 as #1.1, grid size 135,110,101, pixel 0.151,0.151,0.151, shown at level -0.061,0.061, step 1, values float64 > hide #1.1 Opened MO alpha 195 as #1.2, grid size 135,110,101, pixel 0.151,0.151,0.151, shown at level -0.061,0.061, step 1, values float64 > close > open /Users/andrea/Desktop/scratch/ref_eda.out Opened ref_eda.out as an ORCA output file > close > open /Users/andrea/Desktop/scratch/berny_ts_berny_ts0a.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny_ts_berny_ts0a.out --- notes | berny_ts_berny_ts0a.out has 2 imaginary harmonic vibrational modes 97.55i 17.02i Opened berny_ts_berny_ts0a.out as an ORCA output file > ui mousemode right "bond rotation" > torsion /a:1@O6,C16,C15,H29 64.29 > undo Drag select of 4 atoms, 3 bonds [Repeated 1 time(s)]Drag select of 4 atoms, 4 bonds > ui mousemode right "rotate selected models" > view matrix models > #1,0.8648,0.45514,0.21203,-0.036891,-0.50074,0.75057,0.43116,0.093486,0.037093,-0.47905,0.87701,0.052238 > view matrix models > #1,0.84569,0.44808,0.28989,-0.02905,-0.53173,0.75382,0.38603,0.091414,-0.04555,-0.4806,0.87576,0.05699 > view matrix models > #1,0.86934,0.45736,0.18727,-0.039294,-0.49018,0.74962,0.44474,0.094036,0.06302,-0.47843,0.87586,0.050614 > ui mousemode right "translate selected atoms" > select clear Drag select of 1 atoms Drag select of 4 atoms, 3 bonds > select clear Drag select of 4 atoms, 3 bonds > ui tool show "Build QM Input" > select clear > select add /a:1@H31 1 atom, 1 residue, 1 model selected > save /Users/andrea/Desktop/scratch/pre.xyz models #1 > save /Users/andrea/Desktop/scratch/post.xyz models #1 > close > open /Users/andrea/Desktop/scratch/ref_eda.out Opened ref_eda.out as an ORCA output file > close > open /Users/andrea/Desktop/scratch/berny_ts_berny_ts0a.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny_ts_berny_ts0a.out --- notes | berny_ts_berny_ts0a.out has 1 imaginary harmonic vibrational mode 98.21i Opened berny_ts_berny_ts0a.out as an ORCA output file > open /Users/andrea/Desktop/scratch/berny_berny_ts0a.out Summary of feedback from opening /Users/andrea/Desktop/scratch/berny_berny_ts0a.out --- notes | berny_berny_ts0a.out has 1 imaginary harmonic vibrational mode 50.36i Opened berny_berny_ts0a.out as an ORCA output file > close #1 > save /Users/andrea/Desktop/scratch/pre.xyz models #2 > close > open /Users/andrea/Desktop/scratch/ref_eda.out Opened ref_eda.out as an ORCA output file Opened MO alpha 284 as #1.1, grid size 149,110,105, pixel 0.15,0.15,0.15, shown at level -0.061,0.061, step 1, values float64 > hide #1.1 Opened MO alpha 285 as #1.2, grid size 149,110,105, pixel 0.15,0.15,0.15, shown at level -0.061,0.061, step 1, values float64 > hide #1.2 Opened MO alpha 192 as #1.3, grid size 149,110,105, pixel 0.15,0.15,0.15, shown at level -0.061,0.061, step 1, values float64 > hide #1.3 Opened MO alpha 283 as #1.4, grid size 149,110,105, pixel 0.15,0.15,0.15, shown at level -0.061,0.061, step 1, values float64 > close > open /Users/andrea/Desktop/scratch/post_ts_post_ts0a.out Summary of feedback from opening /Users/andrea/Desktop/scratch/post_ts_post_ts0a.out --- note | post_ts_post_ts0a.out has 0 imaginary harmonic vibrational modes Opened post_ts_post_ts0a.out as an ORCA output file Drag select of 1 atoms > select /a:1@H17 1 atom, 1 residue, 1 model selected > select add /a:1@H31 2 atoms, 1 residue, 1 model selected Traceback (most recent call last): File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/tools/input_generator.py", line 887, in update_preview contents, warnings = self.get_file_contents(update_settings=False) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/tools/input_generator.py", line 857, in get_file_contents contents, warnings = self.manager.get_info(program).get_file_contents(self.theory) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/input_file_formats.py", line 960, in get_file_contents header, header_warnings = theory.make_header(style="orca", return_warnings=True) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/theory.py", line 641, in make_header return self.get_orca_header( File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/theory.py", line 1479, in get_orca_header basis_info, basis_warnings = self.basis.get_orca_basis_info() File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/basis.py", line 1014, in get_orca_basis_info import basis_set_exchange as bse File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/__init__.py", line 19, in <module> from .readers import read_formatted_basis_file, read_formatted_basis_str, get_reader_formats File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/__init__.py", line 5, in <module> from .read import read_formatted_basis_file, read_formatted_basis_str, get_reader_formats File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/read.py", line 10, in <module> from .turbomole import read_turbomole File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/turbomole.py", line 3, in <module> from . import helpers File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/helpers.py", line 6, in <module> import regex File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/__init__.py", line 1, in <module> from .regex import * File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/regex.py", line 421, in <module> import regex._regex_core as _regex_core File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex_core.py", line 21, in <module> import regex._regex as _regex ImportError: dlopen(/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so, 0x0002): tried: '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so' (no such file), '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')) ImportError: dlopen(/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so, 0x0002): tried: '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so' (no such file), '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex_core.py", line 21, in import regex._regex as _regex See log for complete Python traceback. Traceback (most recent call last): File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/tools/input_generator.py", line 887, in update_preview contents, warnings = self.get_file_contents(update_settings=False) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/tools/input_generator.py", line 857, in get_file_contents contents, warnings = self.manager.get_info(program).get_file_contents(self.theory) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/input_file_formats.py", line 960, in get_file_contents header, header_warnings = theory.make_header(style="orca", return_warnings=True) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/theory.py", line 641, in make_header return self.get_orca_header( File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/theory.py", line 1479, in get_orca_header basis_info, basis_warnings = self.basis.get_orca_basis_info() File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/basis.py", line 1014, in get_orca_basis_info import basis_set_exchange as bse File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/__init__.py", line 19, in <module> from .readers import read_formatted_basis_file, read_formatted_basis_str, get_reader_formats File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/__init__.py", line 5, in <module> from .read import read_formatted_basis_file, read_formatted_basis_str, get_reader_formats File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/read.py", line 10, in <module> from .turbomole import read_turbomole File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/turbomole.py", line 3, in <module> from . import helpers File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/helpers.py", line 6, in <module> import regex File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/__init__.py", line 1, in <module> from .regex import * File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/regex.py", line 421, in <module> import regex._regex_core as _regex_core File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex_core.py", line 21, in <module> import regex._regex as _regex ImportError: dlopen(/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so, 0x0002): tried: '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so' (no such file), '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')) ImportError: dlopen(/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so, 0x0002): tried: '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so' (no such file), '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex_core.py", line 21, in import regex._regex as _regex See log for complete Python traceback. Traceback (most recent call last): File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/tools/input_generator.py", line 887, in update_preview contents, warnings = self.get_file_contents(update_settings=False) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/tools/input_generator.py", line 857, in get_file_contents contents, warnings = self.manager.get_info(program).get_file_contents(self.theory) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/SEQCROW/input_file_formats.py", line 960, in get_file_contents header, header_warnings = theory.make_header(style="orca", return_warnings=True) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/theory.py", line 641, in make_header return self.get_orca_header( File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/theory.py", line 1479, in get_orca_header basis_info, basis_warnings = self.basis.get_orca_basis_info() File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/AaronTools/theory/basis.py", line 1014, in get_orca_basis_info import basis_set_exchange as bse File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/__init__.py", line 19, in <module> from .readers import read_formatted_basis_file, read_formatted_basis_str, get_reader_formats File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/__init__.py", line 5, in <module> from .read import read_formatted_basis_file, read_formatted_basis_str, get_reader_formats File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/read.py", line 10, in <module> from .turbomole import read_turbomole File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/turbomole.py", line 3, in <module> from . import helpers File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/helpers.py", line 6, in <module> import regex File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/__init__.py", line 1, in <module> from .regex import * File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/regex.py", line 421, in <module> import regex._regex_core as _regex_core File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex_core.py", line 21, in <module> import regex._regex as _regex ImportError: dlopen(/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so, 0x0002): tried: '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so' (no such file), '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')) ImportError: dlopen(/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so, 0x0002): tried: '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')), '/System/Volumes/Preboot/Cryptexes/OS/Users/andrea/Library/Application Support/ChimeraX/1.6/site-packages/regex/_regex.cpython-39-darwin.so' (no such file), '/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex.cpython-39-darwin.so' (mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')) File "/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/_regex_core.py", line 21, in import regex._regex as _regex See log for complete Python traceback. OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGP3T/A Chip: Unknown Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.60.55 OS Loader Version: 10151.60.55 Software: System Software Overview: System Version: macOS 14.2 (23C5041e) Kernel Version: Darwin 23.2.0 Time since boot: 17 days, 14 hours, 12 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal E24-29: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes DELL U2412M: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 argcomplete: 3.0.5 asttokens: 2.2.1 attrs: 22.2.0 Babel: 2.12.1 backcall: 0.2.0 basis-set-exchange: 0.9 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jsonschema: 4.17.3 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 pyrsistent: 0.19.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 regex: 2023.3.23 requests: 2.28.2 scipy: 1.9.3 Send2Trash: 1.8.0 SEQCROW: 1.8.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0
Change History (7)
comment:1 by , 2 years ago
Cc: | added |
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Component: | Unassigned → Tool Shed |
Owner: | set to |
Platform: | → all |
Project: | → ChimeraX |
Status: | new → assigned |
Summary: | ChimeraX bug report submission → Wrong version of regex installed |
comment:2 by , 2 years ago
Cc: | added; removed |
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Owner: | changed from | to
The regex package is not part of ChimeraX, so it looks like a dependency in SEQCROW/AaronTools. So it will need to fixed there. The error, "mach-o file, but is an incompatible architecture (have 'arm64', need 'x86_64')", indicates that is has an arm64 binary when it wanted a x86_64 binary. The macosx packages on pypi.org are only x86_64, so something's odd here.
If AaronTools doesn't actually need the features in regex, it would be much more portable to use Python's re module instead.
comment:3 by , 2 years ago
Owner: | changed from | to
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comment:4 by , 2 years ago
The problem is the reporter is running the Intel Mac ChimeraX on this M1 Mac. I suspect that they installed SEQCROW using the M1 Mac ChimeraX which pulled the M1 regex PyPi package.
The easy fix is to use the M1 Mac ChimeraX which will also be faster on this M1 Mac.
I don't think we can easily handle the user installing Toolshed bundles using Intel ChimeraX and then trying to run them using M1 ChimeraX.
comment:5 by , 2 years ago
Cc: | added |
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Owner: | changed from | to
comment:6 by , 2 years ago
Resolution: | → limitation |
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Status: | assigned → closed |
We can't support installing Toolshed bundles such as SEQCROW using M1 ChimeraX and then trying to run them under Rosetta emulation using Intel ChimeraX.
I can't think of any reason for running Intel ChimeraX on an M1 Mac. But if the reporter really needs that, they should toolshed uninstall SEQCROW and reinstall it with the Intel ChimeraX.
comment:7 by , 2 years ago
I'll defer to Tom on which ChimeraX version should be used for macs. Using the version that is appropriate for your computer is probably the best solution The regex dependency is from the basis-set-exchange module, which was once listed as a dependency for seqcrow. Since seqcrow 1.6.6, it is no longer a dependency because it is quite large and the download would sometimes fail with spottier internet connections. It might still be installed from an older version of seqcrow or if the user installed it manually. The module is convenient if the user is making an input file with a basis set that is not included in their QM software. I can't speak to why they use regex instead of re from the standard library. If you don't want the basis set exchange, you can remove it by running `pip uninstall basis_set_exchange` on the ChimeraX command prompt. Best, Tony On Tue, Nov 28, 2023 at 11:08 AM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> wrote: > > > > >
Reported by Andrea Pellegrini