id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10242 Wrong version of regex installed andreapellegrini6698@… Tom Goddard "{{{ 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 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 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 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 from . import helpers File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/helpers.py"", line 6, in import regex File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/__init__.py"", line 1, in from .regex import * File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/regex.py"", line 421, in 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 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 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 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 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 from . import helpers File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/helpers.py"", line 6, in import regex File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/__init__.py"", line 1, in from .regex import * File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/regex.py"", line 421, in 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 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 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 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 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 from . import helpers File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/basis_set_exchange/readers/helpers.py"", line 6, in import regex File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/__init__.py"", line 1, in from .regex import * File ""/Users/andrea/Library/Application Support/ChimeraX/1.6/site- packages/regex/regex.py"", line 421, in 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 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 }}} " defect closed normal Tool Shed limitation chimera-programmers Greg Couch Tony Schaefer all ChimeraX