id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10013 Crash in Qt event loop: QPainter::begin: Paint device returned engine == 0, type: 3 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000031e4bf000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 576 in _handle_results File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031d4bc000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 528 in _handle_tasks File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031c4b9000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/selectors.py"", line 416 in select File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/connection.py"", line 936 in wait File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 499 in _wait_for_updates File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 519 in _handle_workers File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031b4b6000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x000000031a4b3000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003194b0000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003184ad000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003174aa000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003164a7000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003154a4000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Thread 0x00000003144a1000 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 910 in run File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 973 in _bootstrap_inner File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/threading.py"", line 930 in _bootstrap Current thread 0x0000000202898600 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.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"":""2023-10-17 18:53:28.00 -0700"",""app_version"":""1.6.1"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.2.1 (21D62)"",""incident_id"":""AD706ED2-63EF-4D8C-AB5D-96886A6782A9"",""name"":""ChimeraX""} { ""uptime"" : 930000, ""procLaunch"" : ""2023-10-17 14:57:32.7373 -0700"", ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,3"", ""procStartAbsTime"" : 22018659657488, ""coalitionID"" : 2241, ""osVersion"" : { ""train"" : ""macOS 12.2.1"", ""build"" : ""21D62"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-10-17 18:51:06.6238 -0700"", ""incident"" : ""AD706ED2-63EF-4D8C-AB5D-96886A6782A9"", ""bug_type"" : ""309"", ""pid"" : 30766, ""procExitAbsTime"" : 22354967163067, ""translated"" : true, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.1"",""CFBundleVersion"":""1.6.1.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""58B789E1-901A-570B-A658-90F4780909CF"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""C3F0725F-111E-2832-B2B0-4ABB44C5B9F5"", ""wakeTime"" : 28370, ""sleepWakeUUID"" : ""7CCEC93C-F771-4E06-A7BF-D2F1B31265CC"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. Bytes before following region: 4334497768\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 1025b3000-1025b4000 [ 4K] r-x\/r-x SM=COW ...acOS\/ChimeraX"", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""ktriageinfo"" : ""VM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\nVM - Compressor failed a blocking pager_get\n"", ""vmregioninfo"" : ""0x18 is not in any region. 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""experiments"" : [ { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000017 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/lauriewang/Library/CloudStorage/GoogleDrive- > lauriewang@berkeley.edu/My Drive/2021 - 2023 Park Lab/4. Substrate-engaged > inhibitor bound ChiSec61/3. Structural > modeling/J309_Sec61-KZR779-coot-9_conf1_real_space_refined_001.pdb"" Chain information for J309_Sec61-KZR779-coot-9_conf1_real_space_refined_001.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available > set bgColor white > lighting soft > style ball Changed 4250 atom styles > select /A:501@C30 Nothing selected > select 1/A:501@C30 Expected an objects specifier or a keyword > select #1/A:501@C30 Nothing selected > color /A,B,C gray > color /A:501@C58@O09@C57@C55@C53@C56@C54@C52@C49@C45@N13@C47@C50 blue > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:468 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:410-468 443 atoms, 450 bonds, 59 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > select /C:65 4 atoms, 3 bonds, 1 residue, 1 model selected > select /C 244 atoms, 251 bonds, 31 residues, 1 model selected > select /A:6-7 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:6-43 319 atoms, 327 bonds, 38 residues, 1 model selected > select /A:468 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:351-468 901 atoms, 919 bonds, 118 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /B Alignment identifier is 1/B > select /B:6 5 atoms, 4 bonds, 1 residue, 1 model selected > select /B 480 atoms, 489 bonds, 61 residues, 1 model selected > open ""/Users/lauriewang/Library/CloudStorage/GoogleDrive- > lauriewang@berkeley.edu/My Drive/2021 - 2023 Park Lab/4. Substrate-engaged > inhibitor bound ChiSec61/3. Structural > modeling/J309_Sec61-KZR779-coot-9_conf2_real_space_refined_001.pdb"" Chain information for J309_Sec61-KZR779-coot-9_conf2_real_space_refined_001.pdb #2 --- Chain | Description A | No description available B | No description available C | No description available > hide #!2 models > show #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #2/A Alignment identifier is 1 > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #2/A Alignment identifier is 1 > select #1/A:399-400 #2/A:399-400 30 atoms, 28 bonds, 4 residues, 2 models selected > select #1/A:346-399 #2/A:346-399 832 atoms, 856 bonds, 108 residues, 2 models selected 1 [ID: 1] region 2 chains [327-380] RMSD: 0.000 > select #1/A:432-433 #2/A:432-433 26 atoms, 24 bonds, 4 residues, 2 models selected > select #1/A:432-457 #2/A:432-457 374 atoms, 378 bonds, 52 residues, 2 models selected 1 [ID: 1] region 2 chains [413-438] RMSD: 0.000 > select #1/A:457-458 #2/A:457-458 46 atoms, 48 bonds, 4 residues, 2 models selected > select #1/A:457-468 #2/A:457-468 214 atoms, 218 bonds, 24 residues, 2 models selected 1 [ID: 1] region 2 chains [438-449] RMSD: 0.000 > hide #2.1 models > show #2.1 models > select add #2.1 214 atoms, 218 bonds, 2 pseudobonds, 24 residues, 3 models selected > select subtract #2.1 214 atoms, 218 bonds, 24 residues, 2 models selected > select #1/A:351-468 901 atoms, 919 bonds, 118 residues, 1 model selected > select add #2 5151 atoms, 5262 bonds, 2 pseudobonds, 660 residues, 3 models selected > hide #!1 models > show #!1 models > hide #1.1 models > hide #!1 models > show #!1 models > hide #!2 models > hide #2.1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > close #2 > show #!1 models > show #1.1 models > color /A:501@C58@O09@C57@C55@C53@C56@C54@C52@C49@C45@N13@C47@C50 blue > select /A:501 58 atoms, 62 bonds, 1 residue, 1 model selected > color /A:62-71 violet > color /A:292,183,179,81,85 saddle brown > color /A:300 orange > color /A:127 orangered > color /A:300,127 byhetero > volume zone #2 nearAtoms #1/A:501 range 2 newMap true > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > select /A:462 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:462-467 49 atoms, 48 bonds, 6 residues, 1 model selected > smiles > O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5 Unknown command: smiles O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5 > open smiles > O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5 'smiles' has no suffix > open > smiles:O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5 Translated SMILES to 3D structure via NCI web service (SMILES: O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5) > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #!1 models > select add #2 107 atoms, 110 bonds, 7 residues, 2 models selected > hide #2 models > select subtract #2 49 atoms, 48 bonds, 6 residues, 1 model selected > show #2 models > show #!1 models > hide #1.1 models > hide #!1 models > show #1.1 models > select add #2 107 atoms, 110 bonds, 7 residues, 2 models selected > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > hide #!1 models > select add #1 4308 atoms, 4405 bonds, 2 pseudobonds, 543 residues, 3 models selected > select subtract #1 58 atoms, 62 bonds, 1 residue, 1 model selected > hide #1.1 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Destroying pre-existing alignment with identifier 1/A Alignment identifier is 1/A > show #!1 models > select add #1 4308 atoms, 4405 bonds, 2 pseudobonds, 543 residues, 3 models selected > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > hide #2 target m > close #2 > open ""/Users/lauriewang/Library/CloudStorage/GoogleDrive- > lauriewang@berkeley.edu/My Drive/2021 - 2023 Park Lab/1. hSec61 Inhibitors > Project /5. Model Building and Alphafold Structures/Maps/Unsharpened, Local > Maps/KZR779-Sharpenedmap1(1).mrc"" Opened KZR779-Sharpenedmap1(1).mrc as #2, grid size 600,600,600, pixel 0.83, shown at level 0.0797, step 4, values float32 > volume #2 level 0.2862 > volume #2 step 1 > volume #2 level -0.06033 > volume #2 level 0.1196 > volume #2 level 0.133 > close #2 > show #1.1 models > hide #1.1 models > open /Users/lauriewang/Desktop/cryosparc_P10_J309_007_volume_map.mrc Opened cryosparc_P10_J309_007_volume_map.mrc as #2, grid size 256,256,256, pixel 1.05, shown at level 0.125, step 1, values float32 > volume #2 level 0.3728 > hide #!2 models > select #1/A$501 Expected an objects specifier or a keyword > select #1/@$501 Expected an objects specifier or a keyword > select #1/@501 Expected an objects specifier or a keyword > select #1/A:501 58 atoms, 62 bonds, 1 residue, 1 model selected > select /A:501@C18 1 atom, 1 residue, 1 model selected > select #1/A:501 58 atoms, 62 bonds, 1 residue, 1 model selected > ui tool show ""Selection Inspector"" > ui tool show ""Model Loops"" > select #1/A:501 58 atoms, 62 bonds, 1 residue, 1 model selected > sequence chain #1/A:501 viewer true Expected fewer arguments > sequence chain #1/A:501 Chains must have same sequence > sequence chain #1/A:501 Chains must have same sequence > Unknown command: sequence #1/A:501 > sequence chain #1/A Alignment identifier is 1/A > select /A:468 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:468 7 atoms, 6 bonds, 1 residue, 1 model selected > selection #1/A:501 Unknown command: selection #1/A:501 > select #1/A:501 58 atoms, 62 bonds, 1 residue, 1 model selected > ui tool show ""Selection Inspector"" > color sel #ff40ff atoms > color /A:501@C1 blue > color /A:501@O1 blue > color /A:501@O01 blue > color /A:501@O01 red > structure > O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5 Unknown command: build structure O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5 > start structure > O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5 Unknown command: start structure O=C(NC1=NC([C@@H]2N(C3=CC=C(OC(F)(F)F)C=C3)CCC2)=CS1)C4=CC=CN4CC5=CC=NC=C5 > open ""/Users/lauriewang/Library/CloudStorage/GoogleDrive- > lauriewang@berkeley.edu/My Drive/2021 - 2023 Park Lab/4. Substrate-engaged > inhibitor bound ChiSec61/3. Structural > modeling/J327_Sec61-KZR540-coot-3_conf2_real_space_refined_000.pdb"" Chain information for J327_Sec61-KZR540-coot-3_conf2_real_space_refined_000.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!3 models > show #!1 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > color #1/A:501@C29 > color #1/A:501@C29 blue > color #1/A:501@C29@F32 blue > color #1/A:501@C29@F30@F32 blue > color #1/A:501@C29@F30@F31@F32 blue > color #1/A:501@C26@C29@F30@F31@F32 blue > color #1/A:501@C26@028@C29@F30@F31@F32 blue > color #1/A:501@C26@O28@C29@F30@F31@F32 blue > color #1/A:501@C26@C27@O28@C29@F30@F31@F32 blue > color #1/A:501@C26@C27@O28@C29@F30@F31@F32@C33 blue > color #1/A:501@C25@C26@C27@O28@C29@F30@F31@F32@C33 blue > color #1/A:501@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue > color #1/A:501@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue > color #1/A:501@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue > color #1/A:501@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue > color #1/A:501@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 blue > color #1/A:501@C20@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 > blue > color > #1/A:501@C19@C20@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 > blue > color > #1/A:501@C18@C19@C20@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 > blue > color > #1/A:501@N17@C18@C19@C20@C21@C22@N23@C24@C25@C26@C27@O28@C29@F30@F31@F32@C33@C34 > blue > hide #!1 models > show #!2 models > transparency #2 0.5 > show #!1 models > hide #!2 models > show #!2 models > transparency #2 0.1 > transparency #2 0.9 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > volume zone #2 nearAtoms #1/A:501 range 2 newMap true Opened cryosparc_P10_J309_007_volume_map.mrc zone as #4, grid size 256,256,256, pixel 1.05, shown at step 1, values float32 > surface dust #3 size 5 No surfaces specified > surface dust #3 size 5 No surfaces specified > volume #4 level 0.4534 > color #4 turquoise > transparency #4 0.9 > transparency #4 0.1 > transparency #4 1 > transparency #4.1 0.9 > select add #4.1 58 atoms, 62 bonds, 1 residue, 2 models selected > select subtract #4.1 58 atoms, 62 bonds, 1 residue, 1 model selected > select add #4.1 58 atoms, 62 bonds, 1 residue, 2 models selected > hide #!4 models > show #!4 models > hide #4.1 models > show #4.1 models > dimtransparency #4.1 0.9 Unknown command: dimtransparency #4.1 0.9 > dimtransparency #4 0.9 Unknown command: dimtransparency #4 0.9 > volume #4 style image > transparency #4 0.9 > transparency #4 0.5 > volume #4 style surface > volume #4 change image level 3.945e-05,0 level 0.08594,0.8 level 0.8591,1 > volume #4 level 0.3897 > transparency #4 0.9 > surftransparency #4 90% Unknown command: surftransparency #4 90% > ~surftransparency #4 90% Unknown command: ~surftransparency #4 90% > ~surftransparency #4 Unknown command: ~surftransparency #4 > ~surftransparency Unknown command: ~surftransparency > lighting simple > transparency #4 1 > transparency #4 0.9 > lighting full > lighting soft > lighting full > set bgColor black > set bgColor white > lighting simple > volume #4 level 0.4001 > volume #4 style mesh > volume #4 style image > volume #4 style surface > transparency #4 90 > transparency #4 50 > lighting soft > hide #4.1 models > select subtract #4.1 58 atoms, 62 bonds, 1 residue, 1 model selected > Color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green Unknown command: Color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green > select #1/a:501 58 atoms, 62 bonds, 1 residue, 1 model selected > Color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green Unknown command: Color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green > color #1/A:501@N17@C18@C19@C20@C21@C22@N23 green > color #1/A:501@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36 green > color #1/A:501@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36 green > color #1/A:501@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 green > color #1/A:501@C02@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 green > color #1/A:501@C02@C03@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 > green > color #1/A:501@C02@C03@C04@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 > green > color > #1/A:501@C02@C03@C04@C05@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 > green > color > #1/A:501@C02@C03@C04@C05@C06@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 > green > color > #1/A:501@C02@C03@C04@C05@C06@N07@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 > green > color > #1/A:501@C02@C03@C04@C05@C06@N07@C08@N15@C16@N17@C18@C19@C20@C21@C22@N23@C35@S36@H151 > green > color #1/A:501@C09 blue > color #1/A:501@C09@C10 blue > color #1/A:501@C09@C10@C11 blue > color #1/A:501@C09@C10@C11@N12 blue > color #1/A:501@C09@C10@C11@N12@C13 blue > color #1/A:501@C09@C10@C11@N12@C13@C14 blue > show #4.1 models > lighting soft > lighting simple > lighting soft > lighting full > color /A:62-71 violet > color /A:292,183,179,81,85 saddle brown > lighting soft > color /A:501@O01 orange > volume #4 level 0.1819 > volume #4 level 0.2884 > hide #4.1 models > color /A:501@O01@N17 orange > select #1/A:69 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:69-80 86 atoms, 85 bonds, 12 residues, 1 model selected > select #1/A:64 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:64 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:65 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:65-68 34 atoms, 33 bonds, 4 residues, 1 model selected > select #1/A:66 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:66 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:67 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:67 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:68-69 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1/A:68-69 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1/A:70 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:70-71 11 atoms, 10 bonds, 2 residues, 1 model selected > select #1/A:72 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:72 8 atoms, 7 bonds, 1 residue, 1 model selected > volume #2 level 0.4989 > volume #2 level 0.3788 > volume #2 level 0.4764 > hide #!4 models > show #!4 models > hide #!2 models > volume #2 level 0.3969 > volume #2 level 0.7676 > volume #2 level 0.4884 > volume #2 level 0.4419 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1/A:66 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!2 models > hide #!2 models > hide sel atoms > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1/A:445 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1/A:69 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:66 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:66 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:58 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:58-62 37 atoms, 38 bonds, 5 residues, 1 model selected > select #1/A:70 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:70-73 30 atoms, 29 bonds, 4 residues, 1 model selected > select #1/A:66 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:66-70 39 atoms, 38 bonds, 5 residues, 1 model selected > select #1/A:173 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:173-182 71 atoms, 72 bonds, 10 residues, 1 model selected > select #1/A:173 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:173-174 16 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A:174 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:174 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:170 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:170-184 106 atoms, 107 bonds, 15 residues, 1 model selected > select #1/A:177 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:177-180 24 atoms, 23 bonds, 4 residues, 1 model selected > select #1/A:178 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:178 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:173 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:173-174 16 atoms, 16 bonds, 2 residues, 1 model selected > select #1/A:183 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:183-185 20 atoms, 19 bonds, 3 residues, 1 model selected > select #1/A:182 11 atoms, 11 bonds, 1 residue, 1 model selected > select #1/A:182 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #1/A:181 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:181 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:180 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:180-181 14 atoms, 13 bonds, 2 residues, 1 model selected > show sel atoms > hide sel atoms > select #1/A:178 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:178 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:184 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:184-185 12 atoms, 11 bonds, 2 residues, 1 model selected > select #1/A:185 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:185 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #1/A:182-183 19 atoms, 19 bonds, 2 residues, 1 model selected > select #1/A:182 11 atoms, 11 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #1/A:180 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:180-184 38 atoms, 38 bonds, 5 residues, 1 model selected > select #1/A:180 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:180 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > select #1/A:181 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:181-182 19 atoms, 19 bonds, 2 residues, 1 model selected > select #1/A:182-183 19 atoms, 19 bonds, 2 residues, 1 model selected > select #1/A:182-184 24 atoms, 24 bonds, 3 residues, 1 model selected > select #1/A:184 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:184 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:185 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:185-186 15 atoms, 14 bonds, 2 residues, 1 model selected > select #1/A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:186-187 16 atoms, 15 bonds, 2 residues, 1 model selected > select #1/A:180 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:180 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 76.3 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.9.11 Locale: UTF-8 Qt version: PyQt6 6.4.2, Qt 6.4.2 Qt runtime version: 6.4.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Processor Name: Unknown Processor Speed: 2.4 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache: 16 MB Memory: 16 GB Software: System Software Overview: System Version: macOS 12.2.1 (21D62) Kernel Version: Darwin 21.3.0 Time since boot: 27 days 1:21 Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Family: Supported, Metal GPUFamily Apple 7 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: No Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 build: 0.10.0 certifi: 2021.10.8 cftime: 1.6.2 charset-normalizer: 3.1.0 ChimeraX-AddCharge: 1.5.9.1 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.10 ChimeraX-AtomicLibrary: 10.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.1 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.8 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.9.26 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.5.0 prompt-toolkit: 3.0.38 psutil: 5.9.4 ptyprocess: 0.7.0 pure-eval: 0.2.2 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.4.2 PyQt6-Qt6: 6.4.3 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.3 python-dateutil: 2.8.2 pytz: 2023.3 pyzmq: 25.0.2 qtconsole: 5.4.0 QtPy: 2.3.1 RandomWords: 0.4.0 requests: 2.28.2 scipy: 1.9.3 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.7.0 tcia-utils: 1.2.0 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.1 traitlets: 5.9.0 typing-extensions: 4.5.0 tzdata: 2023.3 urllib3: 1.26.15 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.7 zipp: 3.15.0 }}} " defect closed normal Window Toolkit duplicate Eric Pettersen all ChimeraX