id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15381 Crash changing Mac display configuration wxg622@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit ChimeraX Version: 1.8rc202405202242 (2024-05-20 22:42:21 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff84577efc0 (most recent call first): File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 285 in event_loop File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1006 in init File ""/Applications/ChimeraX-1.8-rc2024.05.20.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1169 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, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.surface._surface, lxml._elementpath, lxml.etree, openmm._openmm, openmm.app.internal.compiled, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 64) {""app_name"":""ChimeraX"",""timestamp"":""2024-06-05 17:29:34.00 +0200"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.5 (23F79)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""793CE7A5-9E1E-4480-8E75-BA56D14D618B""} { ""uptime"" : 170000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 2203, ""osVersion"" : { ""train"" : ""macOS 14.5"", ""build"" : ""23F79"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-06-05 17:29:33.0714 +0200"", ""codeSigningMonitor"" : 0, ""incident"" : ""793CE7A5-9E1E-4480-8E75-BA56D14D618B"", ""pid"" : 63675, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-06-05 12:28:26.0142 +0200"", ""procStartAbsTime"" : 156890247566369, ""procExitAbsTime"" : 174957186112661, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8-rc2024.05.20.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""4C566CA2-7029-58F4-BB6C-330D5EB4C521"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""1E417656-A8B0-359C-066A-118A8C09BB7C"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 26340, ""bridgeVersion"" : {""build"":""21P5077"",""train"":""8.5""}, ""sleepWakeUUID"" : ""3BE4AABB-0D42-4A4C-9CFB-768BC79385A6"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/wxg622/Desktop/T4_final/T4/Contracted/Tip/PDB/fulltip_0_isolde-0.pdb > format pdb Chain information for fulltip_0_isolde-0.pdb #1 --- Chain | Description C D E F G H | No description available I J K L M S | No description available IA IB IC ID IE IK | No description available IM IN IO IP IQ IR | No description available N O P Q R Z | No description available > close > open /Users/wxg622/Desktop/T4_final/Figures/precontracted_composite.cxs > format session Opened B_NU3_P48_J2508_007_volume_map_sharp.mrc as #1, grid size 750,750,750, pixel 1.08, shown at level 0.425, step 1, values float32 Opened NC_P1_NU_P48_J2372_108Apx.mrc as #2, grid size 750,750,750, pixel 1.08, shown at level 0.42, step 1, values float32 Opened cryosparc_P48_cryosparc_P48_J1925_004_volume_map.mrc as #3, grid size 768,768,768, pixel 1.08, shown at level 0.265, step 1, values float32 Opened cryosparc_P48_cryosparc_P48_J1933_003_volume_map.mrc as #5, grid size 540,540,540, pixel 1.08, shown at level 0.321, step 1, values float32 opened ChimeraX session > lighting simple > hide #!1 models > show #!1 models > open > /Users/wxg622/Desktop/T4_final/T4/Extended/Baseplate/maps/J2604_005_volume_map.mrc Opened J2604_005_volume_map.mrc as #4, grid size 750,750,750, pixel 1.08, shown at step 1, values float32 > hide #!1 models > show #!1 models > close #4 > close #1 > open > /Users/wxg622/Desktop/T4_final/T4/Extended/Baseplate/maps/J2604_005_volume_map.mrc Opened J2604_005_volume_map.mrc as #1, grid size 750,750,750, pixel 1.08, shown at step 1, values float32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 region 0,0,0,749,749,749 step 4 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 step 1 > select add #1 3 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,-41.966,0,1,0,27.559,0,0,1,615.97 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > view matrix models > #1,0.86109,0.50841,0.0068025,-193.44,-0.50706,0.85964,-0.062546,307.37,-0.037646,0.050408,0.99802,611.36 > view matrix models > #1,0.86109,0.50841,0.0068025,-193.38,-0.50706,0.85964,-0.062546,297.67,-0.037646,0.050408,0.99802,585.37 > view matrix models > #1,0.86109,0.50841,0.0068025,-148.58,-0.50706,0.85964,-0.062546,270.08,-0.037646,0.050408,0.99802,584.91 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 4 maps. > view matrix models > #1,0.86109,0.50841,0.0068025,-137.19,-0.50706,0.85964,-0.062546,274.98,-0.037646,0.050408,0.99802,568.86 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 0 atomic models, 4 maps. > close > open > /Users/wxg622/Desktop/T4_final/T4/Extended/Neck/PDB/LR_neck_portal_wacs_tail_renamed.cif > format mmcif Summary of feedback from opening /Users/wxg622/Desktop/T4_final/T4/Extended/Neck/PDB/LR_neck_portal_wacs_tail_renamed.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Atom H1 is not in the residue template for ASN /BK:21 Atom H1 is not in the residue template for ASN /BL:21 Atom H is not in the residue template for THR /AA:2 Atom H is not in the residue template for THR /AB:2 Atom H is not in the residue template for VAL /BW:5 Atom H is not in the residue template for THR /AC:2 Atom H is not in the residue template for THR /AD:2 2 messages similar to the above omitted Too many hydrogens missing from residue template(s) to warn about Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for LR_neck_portal_wacs_tail_renamed.cif #1 --- Chain | Description AA AB AC AD AE AF AG AH AI AJ AK AL AM AN AO AP AQ AR | No description available AS AT AU AV AW AX AY AZ BA BB BC BD BE BF BG BH BI BJ | No description available BK BL BM BN BO BP BQ BR BS BT BU BV | No description available BW BX BY BZ CA CB CC CD CE CF CG CH | No description available CI CJ CK CL CM CN CO CP CQ CR CS CT | No description available CU CV CW CX CY CZ | No description available DA DB DC DD DE DF | No description available DG DH DI DJ DK DL | No description available DM DN DO DP DQ DR | No description available 156 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > lighting simple > hide atoms > show cartoons > color /DG,DH,DI,DJ,DK,DL #D8BFD8 > color /CU,CV,CW,CX,CY,CZ #DDA0DD > color /DA,DB,DC,DD,DE,DF #BA55D3 > color /CI,CJ,CK,CL,CM,CN,CO,CP,CQ,CR,CS,CT #9932CC > color /BW,BX,BY,BZ,CA,CB,CC,CD,CE,CF,CG,CH #800080 > color > /AA,AB,AC,AD,AE,AF,AG,AH,AI,AJ,AK,AL,AM,AN,AO,AP,AQ,AR,AS,AT,AU,AV,AW,AX,AY,AZ,BA,BB,BC,BD,BE,BF,BG,BH,BI,BJ > #800000 > color /BK,BL,BM,BN,BO,BP,BQ,BR,BS,BT,BU,BV #87CEFA > color /DM,DN,DO,DP,DQ,DR #1E90FF > select /BN:627 20 atoms, 20 bonds, 1 residue, 1 model selected > select add /BU:425 34 atoms, 33 bonds, 2 residues, 1 model selected Alignment identifier is 1 > select /BN:625 10 atoms, 9 bonds, 1 residue, 1 model selected > select /BN,BU:656 14 atoms, 12 bonds, 2 residues, 1 model selected > select /BN,BU:598-656 1800 atoms, 1818 bonds, 118 residues, 1 model selected > color sel bychain > select /BN:640 19 atoms, 18 bonds, 1 residue, 1 model selected > select clear > select /BN:641 14 atoms, 13 bonds, 1 residue, 1 model selected > select /BN,BU:492-493 34 atoms, 32 bonds, 4 residues, 1 model selected > select /BN,BU:492-493 34 atoms, 32 bonds, 4 residues, 1 model selected > select clear > select /BN:640 19 atoms, 18 bonds, 1 residue, 1 model selected > select /BN,BU:656 14 atoms, 12 bonds, 2 residues, 1 model selected > select /BO:10 19 atoms, 18 bonds, 1 residue, 1 model selected > select /BN:625 10 atoms, 9 bonds, 1 residue, 1 model selected > select /BN:607 16 atoms, 15 bonds, 1 residue, 1 model selected > select /BU:628 21 atoms, 21 bonds, 1 residue, 1 model selected > select /BU:640 19 atoms, 18 bonds, 1 residue, 1 model selected > select /CW:234 12 atoms, 11 bonds, 1 residue, 1 model selected > select up 116 atoms, 116 bonds, 8 residues, 1 model selected > select up 4381 atoms, 4441 bonds, 272 residues, 1 model selected > select up 383010 atoms, 386766 bonds, 24480 residues, 1 model selected > select down 4381 atoms, 4441 bonds, 272 residues, 1 model selected > save /Users/wxg622/Desktop/T4_final/T4/monomers/gp15.pdb selectedOnly true > relModel #1 > open 8HDR Summary of feedback from opening 8HDR fetched from pdb --- note | Fetching compressed mmCIF 8hdr from http://files.rcsb.org/download/8hdr.cif 8hdr title: Cyanophage Pam3 neck [more info...] Chain information for 8hdr #2 --- Chain | Description 1 2 Y Z m n o p q r s t u v w x y z | pam3 tube protein A B C D E F | Pam3 connector protein G H I J K L | Pam3 terminator protein M N O P Q R S T U V W X | Pam3 sheath protein a b c d e f g h i j k l | Pam3 adaptor protein > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #2 to #1 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 LR_neck_portal_wacs_tail_renamed.cif, chain BK (#1) with 8hdr, chain T (#2), sequence alignment score = 145 RMSD between 35 pruned atom pairs is 0.991 angstroms; (across all 310 pairs: 17.689) > matchmaker #2 to #1/BN pairing bs ssFraction 0.754 Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.754 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 LR_neck_portal_wacs_tail_renamed.cif, chain BN (#1) with 8hdr, chain T (#2), sequence alignment score = 730.416 RMSD between 21 pruned atom pairs is 1.298 angstroms; (across all 331 pairs: 27.320) > select clear > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #2/G to #1/BN pairing ss ssFraction 0.754 Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.754 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 LR_neck_portal_wacs_tail_renamed.cif, chain BN (#1) with 8hdr, chain G (#2), sequence alignment score = 244.71 RMSD between 4 pruned atom pairs is 1.190 angstroms; (across all 127 pairs: 26.998) > ui tool show Matchmaker The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > matchmaker #2/G to #1/CW pairing ss ssFraction 0.754 Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.754 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 LR_neck_portal_wacs_tail_renamed.cif, chain CW (#1) with 8hdr, chain G (#2), sequence alignment score = 372.372 RMSD between 21 pruned atom pairs is 0.703 angstroms; (across all 137 pairs: 15.066) > select clear > hide atoms > show cartoons > select #2/G:44 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #1/CW:255 29 atoms, 28 bonds, 2 residues, 2 models selected > select up 168 atoms, 169 bonds, 13 residues, 2 models selected > select up 5628 atoms, 5714 bonds, 428 residues, 2 models selected > select up 461718 atoms, 467076 bonds, 34776 residues, 2 models selected > select down 5628 atoms, 5714 bonds, 428 residues, 2 models selected > select ~sel 456090 atoms, 461362 bonds, 60 pseudobonds, 34348 residues, 3 models selected > hide sel cartoons > select clear > select #1/CW:150 21 atoms, 21 bonds, 1 residue, 1 model selected Alignment identifier is 1/CW > select #1/CW:231 15 atoms, 14 bonds, 1 residue, 1 model selected > select clear > select add #1 383010 atoms, 386766 bonds, 60 pseudobonds, 24480 residues, 2 models selected > select clear > show cartoons > hide #2 models > select #1/DE:150 14 atoms, 13 bonds, 1 residue, 1 model selected Alignment identifier is 1/DE > select #1/DE:178 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/DE:174 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1/DE:174-196 366 atoms, 370 bonds, 23 residues, 1 model selected > select #1/DE:76 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/DE:62 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1/DE:62-83 362 atoms, 366 bonds, 22 residues, 1 model selected > select clear Drag select of 326 residues Drag select of 511 residues Alignment identifier is 1 Alignment identifier is 2 > select clear > select #1/DA-DF:62 84 atoms, 84 bonds, 6 residues, 1 model selected > select #1/DA-DF:62-83 2172 atoms, 2196 bonds, 132 residues, 1 model selected > select clear > color #1 #ebebebff > select #1/DA-DF:62-63 228 atoms, 228 bonds, 12 residues, 1 model selected > select #1/DA-DF:62-82 2112 atoms, 2136 bonds, 126 residues, 1 model selected > color sel purple > select #1/DD:178 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/DA-DF:174-175 234 atoms, 234 bonds, 12 residues, 1 model selected > select #1/DA-DF:175-196 2076 atoms, 2094 bonds, 132 residues, 1 model selected > color sel purple > select #1/DD:222 12 atoms, 11 bonds, 1 residue, 1 model selected > select #1/DA-DF:217-246 2856 atoms, 2880 bonds, 180 residues, 1 model selected > select #1/DA-DF:208-246 3654 atoms, 3684 bonds, 234 residues, 1 model selected > ] Unknown command: ] > color sel purple > select clear > select #1/DD:106 20 atoms, 20 bonds, 1 residue, 1 model selected > select #1/DA-DF:100 132 atoms, 126 bonds, 6 residues, 1 model selected > select #1/DA-DF:100-111 1152 atoms, 1164 bonds, 72 residues, 1 model selected > color sel purple > select #1/CY:184 24 atoms, 23 bonds, 1 residue, 1 model selected > select #1/CU-CZ:176 114 atoms, 108 bonds, 6 residues, 1 model selected > select #1/CU-CZ:176-184 852 atoms, 846 bonds, 54 residues, 1 model selected > color sel green > select #1/CY:72 19 atoms, 18 bonds, 1 residue, 1 model selected > select #1/CU-CZ:51 102 atoms, 96 bonds, 6 residues, 1 model selected > select #1/CU-CZ:51-73 2256 atoms, 2268 bonds, 138 residues, 1 model selected > color sel green > select #1/CY:50 17 atoms, 16 bonds, 1 residue, 1 model selected > select #1/CU-CZ:50 102 atoms, 96 bonds, 6 residues, 1 model selected > select #1/CU-CZ:44-50 684 atoms, 690 bonds, 42 residues, 1 model selected > color sel green > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Unsupported scale factor (0.000000) detected on Display0 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8rc202405202242 (2024-05-20) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.5.17 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 64 GB System Firmware Version: 2022.100.22.0.0 (iBridge: 21.16.5077.0.0,0) OS Loader Version: 580~2215 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 5 days, 6 hours, 53 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-020 Option ROM Version: 113-D32206U1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal PHL 240B7QPJ: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: AU11810007035 Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 7.55 Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 biopython: 1.83 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57 ChimeraX-AtomicLibrary: 14.0.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.4 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: 2.2.4 ChimeraX-Clipper: 0.23.0 ChimeraX-clix: 0.1.5 ChimeraX-ColorActions: 1.0.4 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: 1.8rc202405202242 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.3 ChimeraX-DiffPlot: 1.0 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: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.8.dev0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.16 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-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.4 ChimeraX-PDB: 2.7.5 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: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-QScore: 1.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RIBFIND: 0.2 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: 3.0.4 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.4 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: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.1 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: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.51.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 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: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 ribfind: 2.0.2 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.2 typing-extensions: 4.11.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Window Toolkit duplicate all ChimeraX