Opened 2 years ago

Closed 2 years ago

Last modified 2 years ago

#10242 closed defect (limitation)

Wrong version of regex installed

Reported by: andreapellegrini6698@… 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 Eric Pettersen, 2 years ago

Cc: chimera-programmers Tony Schaefer added
Component: Unassigned → Tool Shed
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Wrong version of regex installed

Reported by Andrea Pellegrini

comment:2 by Greg Couch, 2 years ago

Cc: Greg Couch added; Tony Schaefer removed
Owner: changed from Greg Couch to seqrow

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 Eric Pettersen, 2 years ago

Owner: changed from seqrow to Tony Schaefer

comment:4 by Tom Goddard, 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 Tom Goddard, 2 years ago

Cc: Tony Schaefer added
Owner: changed from Tony Schaefer to Tom Goddard

comment:6 by Tom Goddard, 2 years ago

Resolution: → limitation
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 Tony Schaefer, 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:

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