id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17450 Graphics hardware encountered an error and was reset: chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-x86_64-i386-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. This is an Apple Intel or AMD graphics driver crash that may be related to showing a scene that is complex and uses too much graphics memory. Apple is unlikely to ever fix this since they no longer make computers with Intel or AMD graphics. The crash does not happen with Apple M1,M2,M3... graphics. Fatal Python error: Aborted Thread 0x0000700016e1f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff84e291bc0 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, 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""ad172b80ce89a9052c59d075fb591578b7f2bf6a"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""661464ecda55e5192b100804"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 } ], ""experiments"" : [ { ""treatmentId"" : ""928dfbce-0cc0-4f29-866f-5542e51ad72e"", ""experimentId"" : ""67f46e2984eaf455d73c609a"", ""deploymentId"" : 400000001 }, { ""treatmentId"" : ""f18344bb-554f-48ae-8449-e108a8813a55"", ""experimentId"" : ""6685b5584477001000e8c6c9"", ""deploymentId"" : 400000005 } ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/shukurahanas/Downloads/AF-A0A077FPW4-F1-model_v4.pdb format pdb Summary of feedback from opening /Users/shukurahanas/Downloads/AF-A0A077FPW4-F1-model_v4.pdb --- warning | Ignored bad PDB record found on line 38 DBREF XXXX A 1 220 UNP A0A077FPW4 A0A077FPW4_9RICK 1 220 AF-A0A077FPW4-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for chlamydia protein associating with death domains (A0A077FPW4) [more info...] Chain information for AF-A0A077FPW4-F1-model_v4.pdb #1 --- Chain | Description A | chlamydia protein associating with death domains Computing secondary structure > open 1RCW 1rcw title: Crystal structure of CT610 from Chlamydia trachomatis [more info...] Chain information for 1rcw #2 --- Chain | Description | UniProt A B C | CT610 | PQQCL_CHLTR 1-231 Non-standard residues in 1rcw #2 --- FE — Fe (III) ion 1rcw mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_defined_assembly > select #2/B 1821 atoms, 1789 bonds, 8 pseudobonds, 288 residues, 2 models selected > ui tool show Toolbar > hide sel cartoons > hide sel atoms > select #2/C 1728 atoms, 1742 bonds, 7 pseudobonds, 241 residues, 2 models selected > hide sel cartoons > hide sel atoms > matchmaker #2 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-A0A077FPW4-F1-model_v4.pdb, chain A (#1) with 1rcw, chain A (#2), sequence alignment score = 615.6 RMSD between 197 pruned atom pairs is 0.879 angstroms; (across all 212 pairs: 1.324) > select #1/A: 77 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A: 84 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A: 169 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A: 173 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A: 176 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #1/A: 137 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > set bgColor white > select #1/A 1763 atoms, 1804 bonds, 220 residues, 1 model selected > ui tool show ""Color Actions"" > color sel hot pink > color sel cornflower blue > select #2/A#2/B#2/C 5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected > color sel forest green > color sel cyan > color sel light sea green > color sel purple > color sel hot pink > color sel magenta > color sel light gray > color sel dark gray > color sel gray > color sel dark gray > color sel gray > color sel light gray > color sel gray > color sel dark gray > color sel dim gray > color sel orange > color sel orange red > color sel gray > color sel dark gray > color sel dim gray > ui tool show ""Color Actions"" > color sel light sea green > color sel gray > color sel light slate gray > color sel light salmon > color sel dark goldenrod > color sel olive > color sel tomato > color sel sienna > color sel indian red > color sel sienna > color sel indian red > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""MSE""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 6949 atoms, 7116 bonds, 860 residues, 2 models selected > color sel byhetero > select clear > select ::name=""FE"" 6 atoms, 6 residues, 1 model selected > color sel byhetero > select ::name=""FE""::name=""HOH"" 175 atoms, 2 pseudobonds, 175 residues, 2 models selected > select clear > ui tool show ""Side View"" > save ""/Users/shukurahanas/Desktop/my protein with 1RCW.tif"" width 1984 > height 1137 supersample 3 > open 8VAB Summary of feedback from opening 8VAB fetched from pdb --- notes | Fetching compressed mmCIF 8vab from http://files.rcsb.org/download/8vab.cif Fetching CCD FE2 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/2/FE2/FE2.cif 8vab title: Crystal structure of FeII/FeII CtCADD from Chlamydia trachomatis [more info...] Chain information for 8vab #3 --- Chain | Description | UniProt A | 4-aminobenzoate synthase | CADD_CHLTR 1-220 Non-standard residues in 8vab #3 --- FE2 — Fe (II) ion 8vab mmCIF Assemblies --- 1| author_and_software_defined_assembly > matchmaker #3 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-A0A077FPW4-F1-model_v4.pdb, chain A (#1) with 8vab, chain A (#3), sequence alignment score = 617.5 RMSD between 196 pruned atom pairs is 0.847 angstroms; (across all 213 pairs: 1.313) > hide #!2 models > save ""/Users/shukurahanas/Desktop/MY PROTEİN WİTH 8VAB.tif"" width 1984 > height 1137 supersample 3 > hide #!3 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > save ""/Users/shukurahanas/Desktop/MY PROTEİN WİTH 1RCW.tif"" width 1984 > height 1137 supersample 3 > open 1OTV Summary of feedback from opening 1OTV fetched from pdb --- note | Fetching compressed mmCIF 1otv from http://files.rcsb.org/download/1otv.cif 1otv title: PqqC, Pyrroloquinolinquinone Synthase C [more info...] Chain information for 1otv #4 --- Chain | Description | UniProt A B | Coenzyme PQQ synthesis protein C | PQQC_KLEPN 1-259 1otv mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| software_defined_assembly > matchmaker #4 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-A0A077FPW4-F1-model_v4.pdb, chain A (#1) with 1otv, chain B (#4), sequence alignment score = 363.6 RMSD between 131 pruned atom pairs is 1.167 angstroms; (across all 219 pairs: 3.243) > hide #!2 models > hide #4 models > show #4 models > hide #1 models > close #4 > show #1 models > show #!2 models > show #!3 models > hide #!2 models > open 1OTW Summary of feedback from opening 1OTW fetched from pdb --- notes | Fetching compressed mmCIF 1otw from http://files.rcsb.org/download/1otw.cif Fetching CCD PEO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/PEO/PEO.cif Fetching CCD PQQ from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Q/PQQ/PQQ.cif 1otw title: Crystal structure of PqqC in complex with PQQ and a putative H2O2 [more info...] Chain information for 1otw #4 --- Chain | Description | UniProt A B | Coenzyme PQQ synthesis protein C | PQQC_KLEPN 0-254 Non-standard residues in 1otw #4 --- PEO — hydrogen peroxide PQQ — pyrroloquinoline quinone > matchmaker #4 to #1 Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-A0A077FPW4-F1-model_v4.pdb, chain A (#1) with 1otw, chain A (#4), sequence alignment score = 432.5 RMSD between 157 pruned atom pairs is 1.086 angstroms; (across all 220 pairs: 2.461) > hide #!3 models > select #4/B 2129 atoms, 2154 bonds, 290 residues, 1 model selected > hide sel cartoons > hide sel atoms > hide #4 models > close #4 > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > open /Users/shukurahanas/Downloads/clustalw.aln Summary of feedback from opening /Users/shukurahanas/Downloads/clustalw.aln --- notes | Alignment identifier is clustalw.aln Associated AF-A0A077FPW4-F1-model_v4.pdb chain A to A0A077FPW4 with 0 mismatches Associated 1rcw chain A to O84616 with 0 mismatches Associated 1rcw chain B to O84616 with 0 mismatches Associated 1rcw chain C to O84616 with 0 mismatches Showing conservation header (""seq_conservation"" residue attribute) for alignment clustalw.aln Opened 3 sequences from clustalw.aln > open 2VK8 Summary of feedback from opening 2VK8 fetched from pdb --- notes | Fetching compressed mmCIF 2vk8 from http://files.rcsb.org/download/2vk8.cif Fetching CCD 2OP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/2OP/2OP.cif Fetching CCD TPP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/TPP/TPP.cif 2vk8 title: Crystal structure of the Saccharomyces cerevisiae pyruvate decarboxylase variant E477Q in complex with its substrate [more info...] Chain information for 2vk8 #4 --- Chain | Description | UniProt A B C D | PYRUVATE DECARBOXYLASE ISOZYME 1 | PDC1_YEAST 1-563 Non-standard residues in 2vk8 #4 --- 2OP — (2S)-2-hydroxypropanoic acid MG — magnesium ion TPP — thiamine diphosphate 2vk8 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > hide #1 models > select :20P Nothing selected > select :2OP 24 atoms, 20 bonds, 4 residues, 1 model selected > show sel atoms > select #4/A#4/B#4/C#4/D 19242 atoms, 17787 bonds, 24 pseudobonds, 4078 residues, 2 models selected > color (#!4 & sel) purple > select :2OP 24 atoms, 20 bonds, 4 residues, 1 model selected > color sel byhetero > hide #!4 models > show #!4 models > close #4 > show #1 models Traceback (most recent call last): File ""/Applications/ChimeraX-1.9.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-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/sideview/tool.py"", line 113, in _redraw self.render() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/sideview/tool.py"", line 288, in render self.view.draw() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 188, in draw self._draw_scene(camera, drawings) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/view.py"", line 239, in _draw_scene camera.draw_background(vnum, r) File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/camera.py"", line 195, in draw_background render.draw_background() File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/graphics/opengl.py"", line 1238, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) Error processing trigger ""frame drawn"": OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Unsupported scale factor (0.000000) detected on Display0 > show #!2 models > hide #!2 models > show #!2 models > hide #1 models > select ::name=""HOH"" 201 atoms, 201 residues, 2 models selected > color (#!2 & sel) byhetero > select clear > select #2/A: 82-87 48 atoms, 49 bonds, 6 residues, 1 model selected > color sel byhetero > select #2/A: 82-87 48 atoms, 49 bonds, 6 residues, 1 model selected > color #2/A: 82-87 blue > color #2/A: 82-87 orange > select #2/B 1821 atoms, 1789 bonds, 8 pseudobonds, 288 residues, 2 models selected > show sel cartoons > hide sel atoms > select #2/B 1821 atoms, 1789 bonds, 8 pseudobonds, 288 residues, 2 models selected > hide sel cartoons > show #1 models > color #1/A: 82-87 blue > undo > color #1/A: 78-84 blue > undo > color #1/A: 78-83 blue > color #2/A: 59-85 blue > color #2/A: 59-85 orange > hide #1 models > show #1 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > show #!2 models > save ""/Users/shukurahanas/Desktop/active site of blue and salmon.tif"" width > 1951 height 1263 supersample 3 > hide #!2 models > show #!2 models > hide #1 models > select add #2 5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected > select subtract #2 Nothing selected > select add #2 5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected > select subtract #2 Nothing selected > ui mousemode right label > label delete residues > select clear > show #1 models > hide #1 models > select #2/A: 81 9 atoms, 8 bonds, 1 residue, 1 model selected > color sel byhetero > undo > color sel byhetero > show #1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > select #2/A 1812 atoms, 1781 bonds, 8 pseudobonds, 286 residues, 2 models selected > select add #2 5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected > select subtract #2 Nothing selected > ui mousemode right zoom > ui mousemode right select > select clear > hide #1 models > ui mousemode right distance > ui mousemode right label > label delete residues > select #2/A: 178 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!2 models > show #!2 models > select add #2 5361 atoms, 5312 bonds, 23 pseudobonds, 815 residues, 2 models selected > select subtract #2 Nothing selected > select #2/A: 178 8 atoms, 7 bonds, 1 residue, 1 model selected ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-23.0.26 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655 OpenGL vendor: Intel Inc. Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 8 GB System Firmware Version: 2075.101.2.0.0 (iBridge: 22.16.14248.0.0,0) OS Loader Version: 583~900 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 2 days, 4 hours, 59 minutes Graphics/Displays: Intel Iris Plus Graphics 655: Chipset Model: Intel Iris Plus Graphics 655 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea5 Revision ID: 0x0001 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Mirror: On Mirror Status: Hardware Mirror Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL P2724DEB: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 59.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 1CQRJ04 Main Display: Yes Mirror: On Mirror Status: Master Mirror Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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 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: 1.2.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 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 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 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: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 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: 1.18.1 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 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: 1.41 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: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 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 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Graphics duplicate all ChimeraX