id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18070 Crash using open/save dialog chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.0-arm64-arm-64bit ChimeraX Version: 1.10rc202505100155 (2025-05-10 01:55:54 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00000001eed0f240 (most recent call first): File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 312 in show_open_file_dialog File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py"", line 268 in File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 368 in event_loop File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1057 in init File 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All rights reserved. How to cite UCSF ChimeraX > open ""/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps & > mask/cryosparc_P18_J56_006_volume_map.mrc"" Failed opening file /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA- RNA_hybrid/maps & mask/cryosparc_P18_J56_006_volume_map.mrc: MRC file is truncated. Failed reading 1 values, type int32 > open ""/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps & > mask/cryosparc_P18_J56_006_volume_map_sharp.mrc"" Failed opening file /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA- RNA_hybrid/maps & mask/cryosparc_P18_J56_006_volume_map_sharp.mrc: MRC file is truncated. Failed reading 1 values, type int32 > open ""/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps & > mask/cryosparc_P18_J56_006_volume_map.mrc"" Failed opening file /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA- RNA_hybrid/maps & mask/cryosparc_P18_J56_006_volume_map.mrc: MRC file is truncated. Failed reading 1 values, type int32 > open ""/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps & > mask/cryosparc_P18_J56_006_volume_map_sharp.mrc"" Failed opening file /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA- RNA_hybrid/maps & mask/cryosparc_P18_J56_006_volume_map_sharp.mrc: MRC file is truncated. Failed reading 1 values, type int32 > open ""/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps & > mask/cryosparc_P18_J56_006_volume_map.mrc"" Opened cryosparc_P18_J56_006_volume_map.mrc as #1, grid size 392,392,392, pixel 0.652, shown at level 0.0221, step 2, values float32 > open ""/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA-RNA_hybrid/maps & > mask/cryosparc_P18_J56_006_volume_map_sharp.mrc"" Opened cryosparc_P18_J56_006_volume_map_sharp.mrc as #2, grid size 392,392,392, pixel 0.652, shown at level 0.0346, step 2, values float32 > volume #2 step 1 > volume #2 level 0.05385 > volume #2 color #b9b88f > open /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA- > RNA_hybrid/phenix/RealSpaceRefine_6/8br2_fitted_real_space_refined_006.pdb Chain information for 8br2_fitted_real_space_refined_006.pdb #3 --- Chain | Description A B C D E F | No description available G | No description available H | No description available 132 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > show cartoons > show atoms > hide atoms > show cartoons > transparency #2.1 50 > select nucleic 820 atoms, 918 bonds, 40 residues, 1 model selected > view sel > show sel atoms > hide sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 820 atom styles > color sel byhetero > select clear > select /H:11@C7 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > cofr sel > ui tool show ""Side View"" > show #!1 models > hide #!2 models > volume #1 step 1 > volume #1 level 0.02588 > transparency #1.1 50 > show #!2 models > hide #!1 models > volume #2 level 0.03551 > open /Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51_DNA- > RNA_hybrid/coot/8br2_fitted_real_space_refined_006-coot-2.pdb Chain information for 8br2_fitted_real_space_refined_006-coot-2.pdb #4 --- Chain | Description A B C D E F | No description available G | No description available H | No description available 132 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!3 models > select add #3 15442 atoms, 15624 bonds, 6 pseudobonds, 2044 residues, 2 models selected > select subtract #3 Nothing selected > select add #4 15455 atoms, 15637 bonds, 6 pseudobonds, 2044 residues, 2 models selected > nucleotides sel atoms > style nucleic & sel stick Changed 833 atom styles > color sel byhetero > select protein 28608 atoms, 29016 bonds, 12 pseudobonds, 3732 residues, 4 models selected > show sel & #!4 cartoons > hide sel & #!4 atoms > select clear > volume #2 level 0.04516 > select #4/G:10@N6 1 atom, 1 residue, 1 model selected > select up 21 atoms, 23 bonds, 1 residue, 1 model selected > select up 433 atoms, 492 bonds, 20 residues, 1 model selected > select down 21 atoms, 23 bonds, 1 residue, 1 model selected > select up 433 atoms, 492 bonds, 20 residues, 1 model selected > select clear > select #4/H:11@O2' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #4/G:10@N6 21 atoms, 21 bonds, 2 residues, 1 model selected > select up 41 atoms, 44 bonds, 2 residues, 1 model selected > view sel > select clear > volume #2 level 0.05192 > select #4/H:11@O4 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > view sel > select clear > volume #2 level 0.053 > volume #2 level 0.05 > volume #2 level 0.045 > open 3la5 Summary of feedback from opening 3la5 fetched from pdb --- notes | Fetching compressed mmCIF 3la5 from http://files.rcsb.org/download/3la5.cif Fetching CCD 5AZ from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/5AZ/5AZ.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 3la5 title: X-ray crystal structure of mc6 RNA Riboswitch bound to azacytosine [more info...] Chain information for 3la5 #5 --- Chain | Description A | Adenosine RIboswitch Non-standard residues in 3la5 #5 --- 5AZ — 6-amino-1,3,5-triazin-2(1H)-one (5-Azacytosine) MG — magnesium ion Computing secondary structure Traceback (most recent call last): File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/nucleotides/_data.py"", line 559, in rebuild _rebuild_molecule('internal', mol) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/nucleotides/_data.py"", line 713, in _rebuild_molecule nd.add_shapes(all_shapes) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/shapedrawing.py"", line 297, in add_shapes if atoms is not None and all(atoms.selected): ^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'selected' Error processing trigger ""new frame"": AttributeError: 'list' object has no attribute 'selected' File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/shapedrawing.py"", line 297, in add_shapes if atoms is not None and all(atoms.selected): ^^^^^^^^^^^^^^ See log for complete Python traceback. Failed to send bug report. Error while sending follows: Traceback (most recent call last): File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/bug_reporter/tool.py"", line 253, in submit errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields, timeout=10) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/webservices/post_form.py"", line 43, in post_multipart_formdata h.request('POST', url, body=body, headers=headers) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1286, in request self._send_request(method, url, body, headers, encode_chunked) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1332, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1281, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1041, in _send_output self.send(msg) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 979, in send self.connect() File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 945, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py"", line 851, in create_connection raise exceptions[0] File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py"", line 836, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 61] Connection refused Failed to send bug report. Error while sending follows: Traceback (most recent call last): File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/bug_reporter/tool.py"", line 253, in submit errcode, errmsg, headers, body = post_multipart_formdata(BUG_HOST, BUG_SELECTOR, fields, timeout=10) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/webservices/post_form.py"", line 43, in post_multipart_formdata h.request('POST', url, body=body, headers=headers) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1286, in request self._send_request(method, url, body, headers, encode_chunked) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1332, in _send_request self.endheaders(body, encode_chunked=encode_chunked) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1281, in endheaders self._send_output(message_body, encode_chunked=encode_chunked) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1041, in _send_output self.send(msg) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 979, in send self.connect() File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 945, in connect self.sock = self._create_connection( ^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py"", line 851, in create_connection raise exceptions[0] File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py"", line 836, in create_connection sock.connect(sa) ConnectionRefusedError: [Errno 61] Connection refused > view #5 clip false > hide #!4 models > hide #!2 models > select #5/A:17@N3 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > view sel > select add #5/A:79@N1 21 atoms, 21 bonds, 2 residues, 1 model selected > select up 43 atoms, 46 bonds, 2 residues, 1 model selected > view sel > ui tool show ""Color Actions"" > color sel cornflower blue Traceback (most recent call last): File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/triggerset.py"", line 149, in invoke return self._func(self._name, data) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/nucleotides/_data.py"", line 713, in _rebuild_molecule nd.add_shapes(all_shapes) File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/shapedrawing.py"", line 297, in add_shapes if atoms is not None and all(atoms.selected): ^^^^^^^^^^^^^^ AttributeError: 'list' object has no attribute 'selected' Error processing trigger ""changes"": AttributeError: 'list' object has no attribute 'selected' File ""/Applications/ChimeraX-1.10-rc2025.05.12.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/atomic/shapedrawing.py"", line 297, in add_shapes if atoms is not None and all(atoms.selected): ^^^^^^^^^^^^^^ See log for complete Python traceback. > color sel byhetero > open 9I62 Summary of feedback from opening 9I62 fetched from pdb --- notes | Fetching compressed mmCIF 9i62 from http://files.rcsb.org/download/9i62.cif Fetching CCD ATP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif Fetching CCD CA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/CA/CA.cif 9i62 title: CryoEM structure of a RAD51 D-loop [more info...] Chain information for 9i62 #6 --- Chain | Description | UniProt A B C D E F G H I | DNA repair protein RAD51 homolog 1 | RAD51_HUMAN 1-339 J | DNA (26-MER) | K | DNA (41-MER) | L | DNA (41-MER) | Non-standard residues in 9i62 #6 --- ATP — adenosine-5'-triphosphate CA — calcium ion 44 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > view #6 clip false > hide #!5 models > select add #5 1903 atoms, 1686 bonds, 126 pseudobonds, 464 residues, 3 models selected > show #!6 cartoons > hide #!6 atoms > select nucleic 5360 atoms, 5990 bonds, 177 pseudobonds, 259 residues, 6 models selected > show sel & #!6 atoms > color sel & #!6 byhetero > nucleotides sel & #!6 atoms > style nucleic & sel & #!6 stick Changed 2204 atom styles > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 21 atoms, 23 bonds, 1 residue, 1 model selected > select up 23 atoms, 24 bonds, 2 residues, 1 model selected > view sel > select #6/K:16@N3 1 atom, 1 residue, 1 model selected > select up 22 atoms, 24 bonds, 1 residue, 1 model selected > select add #6/J:18@N3 23 atoms, 24 bonds, 2 residues, 1 model selected > select up 42 atoms, 45 bonds, 2 residues, 1 model selected > view sel > select clear > select #6/J:18@O4 1 atom, 1 residue, 1 model selected > select add #6/K:16@O6 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #6/J:18@O4 #6/K:16@O6 Distance between 9i62 #6/J DT 18 O4 and /K DG 16 O6: 3.408Å > select #6/J:18@N3 1 atom, 1 residue, 1 model selected > select add #6/K:16@N1 2 atoms, 2 residues, 1 model selected > distance #6/J:18@N3 #6/K:16@N1 Distance between 9i62 #6/J DT 18 N3 and /K DG 16 N1: 3.096Å > select #6/J:18@O2 1 atom, 1 residue, 1 model selected > select add #6/K:16@N2 2 atoms, 2 residues, 1 model selected > distance #6/J:18@O2 #6/K:16@N2 Distance between 9i62 #6/J DT 18 O2 and /K DG 16 N2: 2.570Å > ui tool show ""Side View"" > open emdb:52646 Summary of feedback from opening 52646 fetched from emdb --- notes | Fetching compressed map 52646 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-52646/map/emd_52646.map.gz Fetching map header 52646 from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-52646/header/emd-52646.xml Opened emdb 52646 as #8, grid size 416,416,416, pixel 0.652, shown at level 0.017, step 2, values float32, fit PDB 9i62 > volume #8 step 1 > volume #8 color #89aaac > transparency #8.1 50 > volume #8 level 0.02499 > ui tool show ""Side View"" > volume #2 level 0.045 > volume #8 level 0.02765 > open ""/Users/lp212/Dropbox/RAD51/STRUCTURES/RAD51 synapsis/PDB > DEPOSITION/maps/cryosparc_P8_J803_006_volume_map_zflip_sharpenB=75.mrc"" MRC file is truncated. Failed reading 1 values, type int32 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.10rc202505100155 (2025-05-10) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.8.1, Qt 6.8.2 Qt runtime version: 6.8.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac15,6 Model Number: Z1AV0010MB/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 36 GB System Firmware Version: 11881.1.1 OS Loader Version: 11881.1.1 Software: System Software Overview: System Version: macOS 15.0 (24A335) Kernel Version: Darwin 24.0.0 Time since boot: 2 days, 1 hour, 25 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 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 Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.3.0 babel: 2.17.0 beautifulsoup4: 4.13.3 blockdiag: 3.0.0 blosc2: 3.3.2 build: 1.2.2.post1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.2 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.7 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.20.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Aniso: 1.1.3 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.60.5 ChimeraX-AtomicLibrary: 14.1.18 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.5.1 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.2.6 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.10rc202505100155 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 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: 1.4.1 ChimeraX-Hbonds: 2.5.1 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.6.2 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.2.1 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.10.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.19 ChimeraX-ModelPanel: 1.5.1 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14.1 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.10 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.3 ChimeraX-ProfileGrids: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.3 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.7 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.1 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.45.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.2 coverage: 7.8.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.12 debugpy: 1.8.14 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.0 filelock: 3.18.0 fonttools: 4.58.0 funcparserlib: 2.0.0a0 glfw: 2.9.0 grako: 3.16.5 h5py: 3.13.0 html2text: 2024.2.26 idna: 3.10 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.1.0 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.7 jedi: 0.19.1 Jinja2: 3.1.6 jupyter_client: 8.6.3 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.15 kiwisolver: 1.4.8 line_profiler: 4.2.0 lxml: 5.3.1 lz4: 4.4.4 MarkupSafe: 3.0.2 matplotlib: 3.10.1 matplotlib-inline: 0.1.7 msgpack: 1.1.0 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 24.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.4.0 pip: 25.0.1 pkginfo: 1.11.1 platformdirs: 4.3.8 pluggy: 1.5.0 prompt_toolkit: 3.0.51 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.32 Pygments: 2.18.0 pynmrstar: 3.3.5 pynrrd: 1.0.0 PyOpenGL: 3.1.9 PyOpenGL-accelerate: 3.1.9 pyopenxr: 1.1.4501 pyparsing: 3.2.3 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.8.1 PyQt6-Qt6: 6.8.2 PyQt6-WebEngine-commercial: 6.8.0 PyQt6-WebEngine-Qt6: 6.8.2 PyQt6_sip: 13.10.0 pytest: 8.3.5 pytest-cov: 6.1.1 python-dateutil: 2.9.0.post0 pytz: 2025.2 pyzmq: 26.4.0 qtconsole: 5.5.2 QtPy: 2.4.3 qtshim: 1.1 RandomWords: 0.4.0 requests: 2.32.3 roman-numerals-py: 3.1.0 scipy: 1.14.0 setuptools: 78.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.7 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.1.0 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 stack-data: 0.6.3 superqt: 0.7.1 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.13.2 tzdata: 2025.2 urllib3: 2.4.0 wcwidth: 0.2.13 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.14 }}} " defect closed normal UI can't reproduce Tom Goddard all ChimeraX