id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14670 Crash in timer callback chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000031ab68000 (most recent call first): File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 316 in wait File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 574 in wait File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 1297 in run File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x0000000204b05240 (most recent call first): File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/widgets/color_button.py"", line 147 in File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 318 in event_loop File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 870 in init File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1021 in File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/private/var/folders/rh/vkpyxl154wl72fc65qfgldnc0000gp/T/AppTranslocation/7FEA8119-AFF6-4120-BD2E-BF910DBC23BB/d/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2024-02-29 15:19:31.00 -0800"",""app_version"":""1.4.0"",""slice_uuid"":""9596eff5-d2be-396c-9c4e-6177235c3dae"",""build_version"":""1.4.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.1.1 (23B81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""E4D319B0-5E99-47EF-92E0-2320697FF761""} { ""uptime"" : 34000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,3"", ""coalitionID"" : 2289, ""osVersion"" : { ""train"" : ""macOS 14.1.1"", ""build"" : ""23B81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-02-29 15:19:29.6526 -0800"", ""codeSigningMonitor"" : 1, ""incident"" : ""E4D319B0-5E99-47EF-92E0-2320697FF761"", ""pid"" : 49566, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-02-29 15:09:38.2355 -0800"", ""procStartAbsTime"" : 813851813971, ""procExitAbsTime"" : 828045315432, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Volumes\/VOLUME\/*\/ChimeraX-1.4.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.4.0"",""CFBundleVersion"":""1.4.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""8141E164-9F12-59F5-826B-D4D916250B30"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""8C228477-012E-679D-588B-F3CB85AF1965"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 978, ""sleepWakeUUID"" : ""F2159078-9EA8-4A27-A855-8732CA15F0B9"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa1 is not in any region. 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""logWritingSignature"" : ""be0c66989a5778b3e9564e591ee71866130dfef5"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""645c2d2f9e69a025b0a37e29"", ""factorPackIds"" : { }, ""deploymentId"" : 240000003 }, { ""rolloutId"" : ""60f8ddccefea4203d95cbeef"", ""factorPackIds"" : { }, ""deploymentId"" : 240000025 } ], ""experiments"" : [ ] }, ""reportNotes"" : [ ""PC register does not match crashing frame (0x0 vs 0x7FF8ABDBAA78)"" ] } ===== Log before crash start ===== UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/albertoestevez/Documents/SLC_5475_Krios_240205_dataset_maps/8jzx.pdb 8jzx.pdb title: SLC15A4 inhibitor complex [more info...] Chain information for 8jzx.pdb #1 --- Chain | Description | UniProt A B | lysosomal transporter,ALFA tag,lysosomal transporter | S15A4_HUMAN Non-standard residues in 8jzx.pdb #1 --- CLR — cholesterol NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine; 2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine) Q09 — 2-(4-ethoxyphenyl)-N-[3-[(2R)-2-methylpiperidin-1-yl]propyl]quinoline-4-carboxamide > open > /Users/albertoestevez/Documents/SLC_5475_Krios_240205_dataset_maps/emd_36754.mrc Opened emd_36754.mrc as #2, grid size 320,320,320, pixel 0.843, shown at level 0.157, step 2, values float32 > set bgColor white > volume #2 step 1 > volume #2 level 0.3873 > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > view matrix models > #2,0.27917,-0.45783,0.84407,40.96,0.080021,0.88705,0.45468,-58.601,-0.9569,-0.059392,0.28428,235.37 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.27917,-0.45783,0.84407,86.685,0.080021,0.88705,0.45468,-44.583,-0.9569,-0.059392,0.28428,245.33 > view matrix models > #2,0.27917,-0.45783,0.84407,84.251,0.080021,0.88705,0.45468,-37.417,-0.9569,-0.059392,0.28428,246.81 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.31057,-0.59146,0.74413,111.93,0.089887,0.7976,0.59645,-46.362,-0.94629,-0.11835,0.30087,251.03 > view matrix models > #2,0.30483,-0.56769,0.76472,106.64,0.08761,0.81625,0.57102,-45.04,-0.94837,-0.10707,0.29856,250.11 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.30483,-0.56769,0.76472,105.62,0.08761,0.81625,0.57102,-43.796,-0.94837,-0.10707,0.29856,250.22 > surface dust #2 size 8.43 > select add #1 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 4 models selected > fitmap #1 inMap #2 Fit molecule 8jzx.pdb (#1) to map emd_36754.mrc (#2) using 7108 atoms average map value = 0.8295, steps = 76 shifted from previous position = 2.96 rotated from previous position = 4.23 degrees atoms outside contour = 1234, contour level = 0.38729 Position of 8jzx.pdb (#1) relative to emd_36754.mrc (#2) coordinates: Matrix rotation and translation 0.35590430 0.04381424 -0.93349475 201.92532086 -0.52556192 0.83534994 -0.16116805 120.48814659 0.77273333 0.54796970 0.32033173 -132.78289764 Axis 0.36677075 -0.88247250 -0.29448514 Axis point 222.24853050 0.00000000 60.27775468 Rotation angle (degrees) 75.17942156 Shift along axis 6.83541583 > open > /Users/albertoestevez/Downloads/cryosparc_P25_J301_008_volume_map_sharp.mrc Opened cryosparc_P25_J301_008_volume_map_sharp.mrc as #3, grid size 388,388,388, pixel 0.819, shown at level 0.0965, step 2, values float32 > select subtract #2 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 2 models selected > select subtract #1 Nothing selected > volume #3 step 1 > select add #3 2 models selected > surface dust #3 size 8.19 > volume #3 level 0.3161 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.62748,-0.6193,-0.47195,430.51,0.72629,-0.68401,-0.068059,162.76,-0.28067,-0.38548,0.87899,124.69 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.62748,-0.6193,-0.47195,434.37,0.72629,-0.68401,-0.068059,166.15,-0.28067,-0.38548,0.87899,126.12 > view matrix models > #3,-0.62748,-0.6193,-0.47195,440.01,0.72629,-0.68401,-0.068059,160.33,-0.28067,-0.38548,0.87899,125.18 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.46581,-0.77559,-0.426,432,0.85432,-0.51961,0.011869,101.41,-0.23056,-0.35841,0.90465,108.92 > view matrix models > #3,-0.60408,-0.64648,-0.46599,439.68,0.74894,-0.66037,-0.054738,150.89,-0.27234,-0.38207,0.8831,122.67 > view matrix models > #3,-0.61425,-0.63489,-0.46862,439.87,0.7393,-0.67066,-0.060441,154.95,-0.27591,-0.38357,0.88133,123.75 > view matrix models > #3,-0.63501,-0.62998,-0.44708,439.03,0.74377,-0.65497,-0.1335,163.14,-0.20873,-0.4173,0.88447,117.95 > view matrix models > #3,-0.59152,-0.67542,-0.44036,438.29,0.78258,-0.61242,-0.1119,146.84,-0.1941,-0.4108,0.89082,113.6 > view matrix models > #3,-0.61675,-0.69335,-0.37268,434.6,0.76639,-0.63694,-0.083325,148.86,-0.1796,-0.33701,0.92421,94.37 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.61675,-0.69335,-0.37268,435.38,0.76639,-0.63694,-0.083325,146.19,-0.1796,-0.33701,0.92421,93.753 > view matrix models > #3,-0.61675,-0.69335,-0.37268,435.43,0.76639,-0.63694,-0.083325,146.23,-0.1796,-0.33701,0.92421,93.977 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.55147,-0.74542,-0.37447,433.61,0.81923,-0.5686,-0.074599,125.62,-0.15732,-0.34792,0.92423,92.167 > select add #2 4 models selected > select add #1 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 6 models selected Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > select subtract #1 4 models selected > fitmap #2 inMap #3 Fit map emd_36754.mrc in map cryosparc_P25_J301_008_volume_map_sharp.mrc using 63607 points correlation = 0.2577, correlation about mean = 0.03792, overlap = 5627 steps = 80, shift = 0.931, angle = 3.56 degrees Position of emd_36754.mrc (#2) relative to cryosparc_P25_J301_008_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.00557595 0.99991229 -0.01201374 25.23933211 0.07045180 -0.01159126 -0.99744784 284.37587216 -0.99749960 -0.00640811 -0.07038098 292.52952316 Axis 0.59044469 0.58713580 -0.55375683 Axis point 0.00000000 -10.09492083 283.63975613 Rotation angle (degrees) 122.94092929 Shift along axis 19.87946345 > hide #!1 models > select subtract #2 2 models selected > select subtract #3 Nothing selected > volume #3 level 0.3543 > volume #2 level 0.5686 > select add #3 2 models selected > view matrix models > #3,0.5323,-0.62523,0.57075,94.69,-0.62545,-0.7448,-0.23257,407.8,0.5705,-0.23317,-0.7875,225.7 > view matrix models > #3,0.53815,-0.67842,0.50014,113.24,-0.62447,-0.71947,-0.30399,414.78,0.56607,-0.14873,-0.81083,216.63 > view matrix models > #3,0.53581,-0.71219,0.45353,126.26,-0.63441,-0.69403,-0.34036,418,0.55717,-0.10536,-0.82369,213.16 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.53581,-0.71219,0.45353,129.03,-0.63441,-0.69403,-0.34036,413.45,0.55717,-0.10536,-0.82369,216.4 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.41116,-0.79865,0.43944,164.76,-0.75949,-0.56672,-0.31937,409.82,0.5041,-0.20244,-0.83958,242.74 > volume #3 level 0.2875 > select add #2 4 models selected > fitmap #2 inMap #3 Fit map emd_36754.mrc in map cryosparc_P25_J301_008_volume_map_sharp.mrc using 42448 points correlation = 0.6944, correlation about mean = 0.296, overlap = 1.618e+04 steps = 176, shift = 7.28, angle = 25.2 degrees Position of emd_36754.mrc (#2) relative to cryosparc_P25_J301_008_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.03779645 -0.99114721 0.12727385 270.37240997 0.01902014 -0.12662824 -0.99176788 306.93746117 0.99910443 0.03990607 0.01406566 28.41913660 Axis 0.61166081 -0.51689257 0.59890994 Axis point 0.00000000 261.34261245 24.97971910 Rotation angle (degrees) 122.50566993 Shift along axis 23.74301788 > view > volume #3 color #d4ffd8 > volume #3 color #dbffd8 > color #2 #b2d6b2 models transparency 0 > color #2 #b2d6ef models transparency 0 > color #2 #a4d6ef models transparency 0 > show #!1 models > select add #1 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 6 models selected > select subtract #3 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 4 models selected > fitmap #1 inMap #2 Fit molecule 8jzx.pdb (#1) to map emd_36754.mrc (#2) using 7108 atoms average map value = 0.1285, steps = 72 shifted from previous position = 1.05 rotated from previous position = 5.41 degrees atoms outside contour = 6198, contour level = 0.56857 Position of 8jzx.pdb (#1) relative to emd_36754.mrc (#2) coordinates: Matrix rotation and translation 0.42470301 -0.33677990 -0.84036102 230.16960974 -0.28056745 0.83357383 -0.47585352 131.77156832 0.86076086 0.43787438 0.25953184 -121.25774142 Axis 0.47299156 -0.88058632 0.02909839 Axis point 239.97988022 0.00000000 115.62792008 Rotation angle (degrees) 74.99494046 Shift along axis -10.69636399 > select subtract #2 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 2 models selected > view matrix models > #1,0.96681,0.23722,-0.094903,-17.034,-0.20896,0.94789,0.24052,4.5978,0.14701,-0.2127,0.96599,14.981 > view matrix models > #1,0.98736,0.092152,-0.12891,6.9934,-0.059755,0.96998,0.23571,-23.627,0.14677,-0.22503,0.96323,17.345 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.98736,0.092152,-0.12891,7.3786,-0.059755,0.96998,0.23571,-23.396,0.14677,-0.22503,0.96323,17.506 > volume #2 level 0.4012 > view matrix models > #1,0.98736,0.092152,-0.12891,7.4768,-0.059755,0.96998,0.23571,-24.008,0.14677,-0.22503,0.96323,17.445 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.97302,0.19488,-0.1235,-6.6829,-0.10924,0.86063,0.49738,-39.245,0.20322,-0.47047,0.8587,61.658 > select add #2 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 4 models selected > fitmap #1 inMap #2 Fit molecule 8jzx.pdb (#1) to map emd_36754.mrc (#2) using 7108 atoms average map value = 0.2118, steps = 92 shifted from previous position = 4.29 rotated from previous position = 9.01 degrees atoms outside contour = 5167, contour level = 0.40123 Position of 8jzx.pdb (#1) relative to emd_36754.mrc (#2) coordinates: Matrix rotation and translation 0.35291668 0.04867556 -0.93438777 196.48981063 -0.50528220 0.85042055 -0.14654281 112.24610456 0.78748951 0.52384691 0.32472249 -132.46473529 Axis 0.34752703 -0.89261347 -0.28716922 Axis point 216.04511378 0.00000000 58.39038443 Rotation angle (degrees) 74.69068536 Shift along axis 6.13293025 > hide #!3 models > select subtract #2 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 2 models selected > view matrix models > #1,0.97883,0.17618,-0.10415,-8.0318,-0.12282,0.91274,0.38965,-31.126,0.16371,-0.36861,0.91505,47.2 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.97883,0.17618,-0.10415,-8.4053,-0.12282,0.91274,0.38965,-33.027,0.16371,-0.36861,0.91505,43.476 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.97087,0.17243,-0.16634,3.1631,-0.10459,0.92966,0.35326,-33.115,0.21555,-0.32557,0.92062,27.116 > view matrix models > #1,0.93281,0.30582,-0.19061,-7.0459,-0.20671,0.88737,0.41212,-18.23,0.29517,-0.34503,0.89097,21.05 > select add #2 7108 atoms, 7296 bonds, 8 pseudobonds, 918 residues, 4 models selected > fitmap #1 inMap #2 Fit molecule 8jzx.pdb (#1) to map emd_36754.mrc (#2) using 7108 atoms average map value = 0.8295, steps = 96 shifted from previous position = 2.84 rotated from previous position = 7.84 degrees atoms outside contour = 1306, contour level = 0.40123 Position of 8jzx.pdb (#1) relative to emd_36754.mrc (#2) coordinates: Matrix rotation and translation 0.35586111 0.04379850 -0.93351195 201.94158329 -0.52557006 0.83534675 -0.16115810 120.48860211 0.77274768 0.54797583 0.32028661 -132.78238261 Axis 0.36676419 -0.88247778 -0.29447752 Axis point 222.25000249 0.00000000 60.28185783 Rotation angle (degrees) 75.18213331 Shift along axis 6.83785336 > show #!3 models > select subtract #1 2 models selected > select subtract #2 Nothing selected > color #2 #a4d6efbb models > color #3 #dbffd89b models > hide #!3 models > hide #!2 models > show #!3 models > volume #3 level 0.3543 > ui tool show ""Side View"" > volume #3 level 0.6001 > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > volume #3 level 0.6001 > color #3 #dbffc19b models > color #3 #c5ffc19b models > color #3 #c5ffc1bd models > show #!2 models ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.4 (2022-06-03) © 2016-2022 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.3.0, Qt 6.3.0 Qt runtime version: 6.3.0 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGQ3LL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.41.12 OS Loader Version: 10151.41.12 Software: System Software Overview: System Version: macOS 14.1.1 (23B81) Kernel Version: Darwin 23.1.0 Time since boot: 1 day, 5 hours, 33 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 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 LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.3 Babel: 2.10.1 backcall: 0.2.0 blockdiag: 3.0.0 certifi: 2021.10.8 cftime: 1.6.0 charset-normalizer: 2.0.12 ChimeraX-AddCharge: 1.2.3 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2.1 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.4.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.39.1 ChimeraX-AtomicLibrary: 7.0 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.1 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.1 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.7 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.18.0 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.1 ChimeraX-CommandLine: 1.2.3 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.4 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.1 ChimeraX-DistMonitor: 1.1.5 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.2 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.4 ChimeraX-ItemsInspection: 1.0 ChimeraX-Label: 1.1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.6 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.7 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.5.5 ChimeraX-ModelPanel: 1.3.2 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-NIHPresets: 1.1.17 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.9 ChimeraX-PDB: 2.6.6 ChimeraX-PDBBio: 1.0 ChimeraX-PDBImages: 1.2 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-Phenix: 0.3 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 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 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StarMap: 1.2.15 ChimeraX-StdCommands: 1.8 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.0.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.1 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.18.3 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.1.0 ChimeraX-XMAS: 1.1.2 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.2 cycler: 0.11.0 Cython: 0.29.26 debugpy: 1.6.0 decorator: 5.1.1 docutils: 0.17.1 entrypoints: 0.4 et-xmlfile: 1.1.0 filelock: 3.4.2 fonttools: 4.33.3 funcparserlib: 1.0.0 grako: 3.16.5 h5py: 3.7.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.27 imagecodecs: 2021.11.20 imagesize: 1.3.0 ipykernel: 6.6.1 ipython: 7.31.1 ipython-genutils: 0.2.0 jedi: 0.18.1 Jinja2: 3.0.3 jupyter-client: 7.1.0 jupyter-core: 4.10.0 kiwisolver: 1.4.2 line-profiler: 3.4.0 lxml: 4.7.1 lz4: 3.1.10 MarkupSafe: 2.1.1 matplotlib: 3.5.1 matplotlib-inline: 0.1.3 msgpack: 1.0.3 nest-asyncio: 1.5.5 netCDF4: 1.5.8 networkx: 2.6.3 numexpr: 2.8.1 numpy: 1.22.1 openpyxl: 3.0.10 openvr: 1.16.802 packaging: 21.0 pandas: 1.5.2 ParmEd: 3.4.3 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.0.1 pip: 21.3.1 pkginfo: 1.8.2 prompt-toolkit: 3.0.29 psutil: 5.9.0 ptyprocess: 0.7.0 pycollada: 0.7.2 pydicom: 2.2.2 Pygments: 2.11.2 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 PyQt6-commercial: 6.3.0 PyQt6-Qt6: 6.3.0 PyQt6-sip: 13.3.1 PyQt6-WebEngine-commercial: 6.3.0 PyQt6-WebEngine-Qt6: 6.3.0 pyqtgraph: 0.13.1 python-dateutil: 2.8.2 pytz: 2022.1 pyzmq: 23.1.0 qtconsole: 5.3.0 QtPy: 2.1.0 QtRangeSlider: 0.1.5 RandomWords: 0.3.0 requests: 2.27.1 scipy: 1.7.3 seaborn: 0.12.1 Send2Trash: 1.8.2 SEQCROW: 1.8.7 setuptools: 59.8.0 sfftk-rw: 0.7.2 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.3.2 sphinx-autodoc-typehints: 1.15.2 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-community: 1.0.0 tables: 3.7.0 tifffile: 2021.11.2 tinyarray: 1.2.4 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.9 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.1 wheel-filename: 1.3.0 }}} " defect closed normal Core can't reproduce all ChimeraX