id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10238 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 minhducdkh@… Eric Pettersen "{{{ 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 Current thread 0x00007ff85507db40 (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"":""2023-11-27 19:59:51.00 +0100"",""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 14.1.1 (23B81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""1BBBD5A3-934E-4958-BE29-6B8DA4DD2E2C""} { ""uptime"" : 210000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 7791, ""osVersion"" : { ""train"" : ""macOS 14.1.1"", ""build"" : ""23B81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-11-27 19:59:44.5232 +0100"", ""codeSigningMonitor"" : 0, ""incident"" : ""1BBBD5A3-934E-4958-BE29-6B8DA4DD2E2C"", ""pid"" : 13677, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-11-24 15:59:21.2704 +0100"", ""procStartAbsTime"" : 8093456760410, ""procExitAbsTime"" : 214554127324919, ""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"":""1B621CC7-A08E-58E5-A30C-B64306F232D4"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""5A8EFE95-C9B8-50CB-3111-3AE68D059CBA"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 27642, ""bridgeVersion"" : {""build"":""21P1069"",""train"":""8.1""}, ""sleepWakeUUID"" : ""592314B4-3C69-449D-9048-A364D68F692D"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. Bytes before following region: 140737488089064\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7ffffffbf000-7ffffffc0000 [ 4K] r-x\/r-x SM=SHM "", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":13677}, ""ktriageinfo"" : ""VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n"", ""vmregioninfo"" : ""0x18 is not in any region. 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the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM- > fromAsitetoPsite/tige-LSU-novel-different-AP-tRNA.cxs format session opened ChimeraX session > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > hide #!11 models > hide #7 models > hide #4 models > hide #13 models > hide #8 models > show #8 models > hide #8 models > show #8 models > show #4 models > hide #4 models > show #4 models > hide #4,6,8,10,12,14 atoms > select add #6 42 atoms, 45 bonds, 1 residue, 1 model selected > show sel atoms > select subtract #6 Nothing selected > show #7 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #7 models > show #7 models > hide #7 models > hide #4 models > hide #10 models > select #8/Aw:71 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > nucleotides sel atoms > style sel sphere Changed 31 atom styles > select #8/Aw:69 33 atoms, 35 bonds, 1 residue, 1 model selected > select #8/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > select add #8 2161 atoms, 2330 bonds, 68 residues, 1 model selected > select subtract #8 Nothing selected > select add #8 2161 atoms, 2330 bonds, 68 residues, 1 model selected > nucleotides sel atoms > style sel sphere Changed 2161 atom styles > select clear > select #8/Aw:69 33 atoms, 35 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select add #12 42 atoms, 45 bonds, 1 residue, 1 model selected > show sel atoms > select clear > open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM- > fromAsitetoPsite/hybrid-tRNA-mitoribosome-7qi6.pdb Summary of feedback from opening /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM- fromAsitetoPsite/hybrid-tRNA-mitoribosome-7qi6.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 GLUAB 53 LEUAB 63 1 11 Start residue of secondary structure not found: HELIX 2 2 ASNAB 64 HISAB 69 1 6 Start residue of secondary structure not found: HELIX 3 3 ASNAB 74 PHEAB 79 1 6 Start residue of secondary structure not found: HELIX 4 4 SERAB 80 ALAAB 87 1 8 Start residue of secondary structure not found: HELIX 5 5 GLYAB 96 ARGAB 98 1 3 1011 messages similar to the above omitted Cannot find LINK/SSBOND residue CYSA (45 ) Cannot find LINK/SSBOND residue 5F0A (184 ) Cannot find LINK/SSBOND residue A (76 ) Cannot find LINK/SSBOND residue C (2437 ) Cannot find LINK/SSBOND residue A (2451 ) 898 messages similar to the above omitted Chain information for hybrid-tRNA-mitoribosome-7qi6.pdb #15 --- Chain | Description Aw | No description available > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > hide sel cartoons > nucleotides sel fill > nucleotides sel atoms > hide sel atoms > show sel cartoons > hide #8 models > select clear > select #15/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > hide sel atoms > show sel atoms > hide sel cartoons > select #15/Aw:71 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > select subtract #15 Nothing selected > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > hide sel cartoons > show #8 models > select #8/Aw:69@OP1 1 atom, 1 residue, 1 model selected > select up 33 atoms, 35 bonds, 1 residue, 1 model selected > hide sel atoms > select clear > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > hide H > select clear > show #7 models > show #!9 models > select add #9 1482 atoms, 1655 bonds, 1 pseudobond, 70 residues, 2 models selected > ui tool show ""Color Actions"" > color sel forest green > color #9 #228b2246 > color #9 #228b224c > color #9 #228b2230 > select clear > color #7 #7a81ffff > color #7 #7a81ff77 > color #7 #7a81ff8e > select clear > color #7 #7a81ff8f > color #15 #73fdffff > select clear > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > color sel byhetero > select clear > hide #15 models > show #15 models > hide #!9 models > show #!9 models > hide #!9 models > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM- > fromAsitetoPsite/figure-tige-LSU-1-tRNA-3.tif width 1201 height 757 > supersample 3 > show #!9 models > hide #6-8,12,14-15#!9 atoms > select add #12 42 atoms, 45 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color #12 #ff40ffff > select clear > select add #6 42 atoms, 45 bonds, 1 residue, 1 model selected > show sel atoms > select clear > color #6 #ff40ffff > select add #6 42 atoms, 45 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > color #6 #ff40ff3c > color #6 #ff40ff2e > select clear > color #6 #ff40ff29 > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM- > fromAsitetoPsite/figure-tige-LSU-1-tRNA-1.tif width 1201 height 757 > supersample 3 transparentBackground true > color #9 #228b2277 > color #9 #228b2280 > color #9 #228b2270 > color #7 #7a81ffbc > color #7 #7a81ffb8 > select add #7 2165 atoms, 2328 bonds, 74 residues, 1 model selected > color sel medium blue > color #7 #7a81ffde > ui tool show ""Color Actions"" > color sel medium blue > color #7 #0000cd8d > color #7 #0000cd8c > select clear > select add #7 2165 atoms, 2328 bonds, 74 residues, 1 model selected > color sel blue > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM- > fromAsitetoPsite/figure-tige-LSU-1-tRNA-1.tif width 1201 height 757 > supersample 3 transparentBackground true > color #6 #ff40ff5d > color #6 #ff40ff69 > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM- > fromAsitetoPsite/figure-tige-LSU-1-tRNA-1.tif width 1201 height 757 > supersample 3 transparentBackground true > select add #12 42 atoms, 45 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > color #6 #ff40ff2e > color #6 #ff40ff26 > select clear > select #8/Aw:71 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > select #8/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > select #8/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > select clear > hide #!9 models > hide #15 models > show #15 models > show #6-8,12,14-15 atoms > hide #6-8,12,14-15 atoms > show #6-8,12,14-15 atoms > hide #6-8,12,14-15 atoms > hide #15 models > show #15 models > show #6-8,12,14-15 cartoons > hide #8 models > select #15/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > select #15/Aw:69 33 atoms, 35 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > select #15/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > show #8 models > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > hide sel cartoons > select clear > select #8/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > select #8/Aw:69 33 atoms, 35 bonds, 1 residue, 1 model selected > show sel atoms > hide H > select add #12 75 atoms, 80 bonds, 2 residues, 2 models selected > show sel atoms > select add #8 2203 atoms, 2375 bonds, 69 residues, 2 models selected > select subtract #8 42 atoms, 45 bonds, 1 residue, 1 model selected > select add #6 84 atoms, 90 bonds, 2 residues, 2 models selected > show sel atoms > select clear > select #8/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > select #8/Aw:71 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > select #8/Aw:69@H4' 1 atom, 1 residue, 1 model selected > select up 33 atoms, 35 bonds, 1 residue, 1 model selected > hide sel atoms > select #15/Aw:69@O4' 1 atom, 1 residue, 1 model selected > select up 33 atoms, 35 bonds, 1 residue, 1 model selected > hide sel atoms > hide #8 models > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > select subtract #15 Nothing selected > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > select clear > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > show sel cartoons > select #15/Aw:70 31 atoms, 32 bonds, 1 residue, 1 model selected > select #15/Aw:71 31 atoms, 32 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > select subtract #15 Nothing selected > select add #15 2161 atoms, 2330 bonds, 68 residues, 1 model selected > hide sel cartoons > select clear > show #8 models > select add #12 42 atoms, 45 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel brown > color sel purple > color sel byhetero > select subtract #12 Nothing selected > select add #6 42 atoms, 45 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color sel purple > select clear > hide H > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tRNA-EM- > fromAsitetoPsite/figure-tige-LSU-1-tRNA-3.tif width 1201 height 757 > supersample 3 transparentBackground true > open ""/Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/tigecycline-bound > compare WT mitoribosome.cxs"" opened ChimeraX session > ui tool show ""Side View"" > show #!6 models > hide #!6 models Drag select of 2374 residues > select up 43541 atoms, 46523 bonds, 3762 residues, 1 model selected > select up 56207 atoms, 59472 bonds, 5309 residues, 1 model selected > select up 56265 atoms, 59532 bonds, 5313 residues, 1 model selected > select up 176233 atoms, 184658 bonds, 18240 residues, 1 model selected > select down 56265 atoms, 59532 bonds, 5313 residues, 1 model selected > select clear Drag select of 4592 residues > select up 56516 atoms, 59770 bonds, 5344 residues, 1 model selected > select up 68446 atoms, 71964 bonds, 6804 residues, 1 model selected > color sel yellow > select clear > select #1/AA:1536 22 atoms, 24 bonds, 1 residue, 1 model selected > select up 20260 atoms, 22661 bonds, 954 residues, 1 model selected > color sel light gray > select clear > lighting simple Drag select of 4082 residues > select up 68874 atoms, 73807 bonds, 5853 residues, 1 model selected > select up 82452 atoms, 87737 bonds, 7495 residues, 1 model selected > select up 82555 atoms, 87844 bonds, 7500 residues, 1 model selected > select up 176233 atoms, 184658 bonds, 18240 residues, 1 model selected > select down 82555 atoms, 87844 bonds, 7500 residues, 1 model selected > select clear Drag select of 5455 residues > select up 77566 atoms, 82709 bonds, 6902 residues, 1 model selected > select up 88659 atoms, 94092 bonds, 8247 residues, 1 model selected > select up 88762 atoms, 94199 bonds, 8252 residues, 1 model selected > select up 176233 atoms, 184658 bonds, 18240 residues, 1 model selected > select down 88762 atoms, 94199 bonds, 8252 residues, 1 model selected > hide #8 models > select clear Drag select of 6335 residues > select up 82357 atoms, 87599 bonds, 7498 residues, 1 model selected > select up 93223 atoms, 98741 bonds, 8808 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light sky blue > color sel sky blue > select clear > select add #1 176233 atoms, 184658 bonds, 23 pseudobonds, 18240 residues, 3 models selected > cartoon style (#!1 & sel) modeHelix tube sides 20 > select clear > select #1/A:2609 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 33028 atoms, 36953 bonds, 1556 residues, 1 model selected > color sel dark gray > select clear > select #1/AA:822 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 20260 atoms, 22661 bonds, 954 residues, 1 model selected > select clear > show #8 models > color #8 #8efa00ff > select clear Drag select of 3550 residues > select clear > select #1/A:6552@C1B 1 atom, 1 residue, 1 model selected > select up 42 atoms, 45 bonds, 1 residue, 1 model selected > style sel sphere Changed 42 atom styles > ui tool show ""Color Actions"" > color sel brown > color sel byhetero > color sel coral > color sel byhetero > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige- > bound.pdb models #1 selectedOnly true relModel #1 > open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige- > bound.pdb Summary of feedback from opening /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige- bound.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 184 ALA D 186 1 3 Start residue of secondary structure not found: HELIX 2 2 HIS D 252 LYS D 254 1 3 Start residue of secondary structure not found: HELIX 3 3 ALA D 260 ARG D 262 1 3 Start residue of secondary structure not found: HELIX 4 4 ASN D 263 TRP D 265 1 3 Start residue of secondary structure not found: HELIX 5 5 ASN E 57 LEU E 73 1 17 996 messages similar to the above omitted Cannot find LINK/SSBOND residue FES (201 ) Cannot find LINK/SSBOND residue FES (201 ) > select ::name=""T1C"" 168 atoms, 180 bonds, 4 residues, 2 models selected > hide sel atoms > select add #1 176275 atoms, 184703 bonds, 23 pseudobonds, 18241 residues, 4 models selected > select subtract #1 42 atoms, 45 bonds, 1 residue, 1 model selected > select subtract #5 Nothing selected > select add #5 42 atoms, 45 bonds, 1 residue, 1 model selected > show sel atoms > ui tool show ""Color Actions"" > select clear > select #1/Ax:45 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 1482 atoms, 1655 bonds, 70 residues, 1 model selected > color sel forest green > select clear > select #1/Ax:45 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 1482 atoms, 1655 bonds, 70 residues, 1 model selected > lighting simple > select clear > color #8 #ff40ffff > select clear > select #1/L:130 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 52 atoms, 51 bonds, 6 residues, 1 model selected > select up 890 atoms, 905 bonds, 115 residues, 1 model selected > color #8 #00fdffff > color #8 #ff40ffff > select clear > color #1,5,8 light sea green > undo > select clear > select #1/L:129 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 52 atoms, 51 bonds, 6 residues, 1 model selected > select up 890 atoms, 905 bonds, 115 residues, 1 model selected > ui tool show ""Color Actions"" Drag select of 925 residues > select up 41888 atoms, 46024 bonds, 2647 residues, 1 model selected > select clear > select ::name=""T1C"" 168 atoms, 180 bonds, 4 residues, 2 models selected > show sel atoms > color sel purple > ui tool show ""Color Actions"" > style sel sphere Changed 168 atom styles > color sel byhetero > select clear > select #1/L:136 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 3 residues, 1 model selected > select up 890 atoms, 905 bonds, 115 residues, 1 model selected > color sel #00fdffff > color sel #73fdffff > color sel #73fcd6ff > select clear > select #1/L:136 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 22 atoms, 21 bonds, 3 residues, 1 model selected > select up 890 atoms, 905 bonds, 115 residues, 1 model selected > color #1 #73fdffff > undo > color sel #73fdffff > color sel #73fdffed > color sel #73fdffc6 > color sel #73fdffbb > color sel #73fdffba > color sel #73fdffab > color sel #73fdffa8 > color sel #73fdffa4 > color sel #73fdffa1 > color sel #73fdff9d > color sel #73fdff99 > color sel #73fdff97 > color sel #73fdff96 > color sel #73fdff95 > color sel #73fdff90 > color sel #73fdff8c > color sel #73fdff88 > color sel #73fdff85 > color sel #73fdff82 > color sel #73fdff81 > color sel #73fdff7d > color sel #73fdff7c > color sel #73fdff7a > color sel #73fdff78 > color sel #73fdff76 > color sel #73fdff73 > color sel #73fdff70 > color sel #73fdff6f > color sel #73fdff6c > color sel #73fdff69 > color sel #73fdff66 > color sel #73fdff64 > color sel #73fdff63 > select clear > select #1/Ax:44 22 atoms, 24 bonds, 1 residue, 1 model selected > select up 1482 atoms, 1655 bonds, 70 residues, 1 model selected > color sel #73fdff64 > color sel #73fdff66 > color sel #73fdff6c > color sel #73fdff70 > color sel #73fdff80 > color sel #73fdff88 > color sel #73fdff8d > color sel #73fdff95 > color sel #73fdff9a > color sel #73fdff9d > color sel #73fdff9f > color sel #73fdffa2 > color sel #73fdffa5 > color sel #73fdffab > color sel #73fdffb0 > color sel #73fdffb5 > color sel #73fdffb8 > color sel #73fdffbd > color sel #73fdffc3 > color sel #73fdffca > color sel #73fdffce > color sel #73fdffcf > color sel #73fdffd0 > color sel #73fdffd1 > color sel #73fdffd7 > color sel #73fdffdc > color sel #73fdffdf > color sel #73fdffe4 > color sel #73fdffe6 > color sel #73fdffe7 > color sel #73fdffe8 > select clear > select #1/Ax:45 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 1482 atoms, 1655 bonds, 70 residues, 1 model selected > color sel forest green > select clear > select #1/Ax:45 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 1482 atoms, 1655 bonds, 70 residues, 1 model selected > color sel #73fdffe9 > color sel #73fdffef > color sel #73fdfff6 > color sel #73fdfffa > color sel #73fdfffb > color sel #73fdfff0 > color sel #73fdffe1 > color sel #73fdffd1 > color sel #73fdffd0 > color sel #73fdffd1 > color sel #00f900ff > select clear > select #1/Ax:45 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 1482 atoms, 1655 bonds, 70 residues, 1 model selected > ui tool show ""Color Actions"" > select clear > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/RRF.cxs > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall- > RRFbound.tif width 1201 height 757 supersample 3 transparentBackground true > select #1/AA:1557 22 atoms, 24 bonds, 1 residue, 1 model selected > select up 20260 atoms, 22661 bonds, 954 residues, 1 model selected > select up 20302 atoms, 22706 bonds, 955 residues, 1 model selected > select up 176233 atoms, 184658 bonds, 18240 residues, 1 model selected > select down 20302 atoms, 22706 bonds, 955 residues, 1 model selected > hide sel > select #1/Ax:67 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 1482 atoms, 1655 bonds, 70 residues, 1 model selected > hide sel > hide cartoons target a > undo > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/P-tRNA.pdb > models #1 selectedOnly true relModel #1 > delete sel > select #1/A:6553@C6 1 atom, 1 residue, 1 model selected > select up 42 atoms, 45 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:6552@C42 1 atom, 1 residue, 1 model selected > select up 42 atoms, 45 bonds, 1 residue, 1 model selected > color sel #00f900ff > color sel #00f900dc > color sel #00f900c1 > color sel #00f900ae > color sel #00f900b0 > color sel #00f900ae > color sel #00f9008d > color sel #00f90066 > color sel #942192ff > color sel byhetero > color sel #942192ff > color sel #942192f3 > color sel #942192d1 > color sel #942192c8 > color sel #942192be > color sel #942192b4 > color sel #942192ae > color sel #942192a8 > color sel #942192a0 > color sel #94219296 > color sel #94219280 > color sel #94219270 > color sel #9421926c > color sel #94219265 > color sel #9421925e > color sel #94219257 > color sel #94219253 > color sel #9421924d > color sel #9421924c > color sel #9421924a > color sel #94219242 > color sel #9421923f > color sel #9421923c > color sel #9421923b > color sel #9421923c > color sel #94219247 > color sel #9421924f > color sel #94219251 > select #1/M:134 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:6552@C42 1 atom, 1 residue, 1 model selected > select up 42 atoms, 45 bonds, 1 residue, 1 model selected > open /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige- > bound.pdb Summary of feedback from opening /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/LSU-1-tige- bound.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 LEU D 184 ALA D 186 1 3 Start residue of secondary structure not found: HELIX 2 2 HIS D 252 LYS D 254 1 3 Start residue of secondary structure not found: HELIX 3 3 ALA D 260 ARG D 262 1 3 Start residue of secondary structure not found: HELIX 4 4 ASN D 263 TRP D 265 1 3 Start residue of secondary structure not found: HELIX 5 5 ASN E 57 LEU E 73 1 17 996 messages similar to the above omitted Cannot find LINK/SSBOND residue FES (201 ) Cannot find LINK/SSBOND residue FES (201 ) > transparency sel 60 target a > select clear > select #1/AJ:78 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 69 atoms, 68 bonds, 8 residues, 1 model selected > select up 839 atoms, 855 bonds, 108 residues, 1 model selected > transparency sel 80 target a > select #1/A:6552@C42 1 atom, 1 residue, 1 model selected > select up 42 atoms, 45 bonds, 1 residue, 1 model selected > transparency sel 80 target a > color sel light gray > style sel sphere Changed 42 atom styles > style sel stick Changed 42 atom styles > style sel stick Changed 42 atom styles > select #5/A:6552@C42 1 atom, 1 residue, 1 model selected > select up 42 atoms, 45 bonds, 1 residue, 1 model selected > style sel stick Changed 42 atom styles > style sel sphere Changed 42 atom styles > hide #9 models > show #9 models > hide #9 models > show #9 models > hide sel atoms > show sel atoms > color sel light gray > transparency sel 80 target a > select clear > color #9 #942192ff > select add #9 42 atoms, 45 bonds, 1 residue, 1 model selected > color sel byhetero > select clear > select #1/A:2625 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 33028 atoms, 36953 bonds, 1556 residues, 1 model selected > select clear > select #1/A:2625 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 33028 atoms, 36953 bonds, 1556 residues, 1 model selected > transparency sel 80 target a > select clear > select #1/A:2626 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 33028 atoms, 36953 bonds, 1556 residues, 1 model selected > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 509326 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > hide sel atoms > select clear > select #1/AA:1495 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 20260 atoms, 22661 bonds, 954 residues, 1 model selected > hide sel atoms > select #1/A:2580 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 33028 atoms, 36953 bonds, 1556 residues, 1 model selected > hide sel cartoons > select #1/H:76 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 43 atoms, 43 bonds, 4 residues, 1 model selected > select up 1661 atoms, 1698 bonds, 202 residues, 1 model selected > select up 174751 atoms, 183003 bonds, 18170 residues, 1 model selected > hide sel cartoons > select clear Drag select of 36 atoms, 34 bonds, 11 shapes > select up 85 atoms, 93 bonds, 6 residues, 1 model selected > hide sel atoms > hide sel cartoons Drag select of 7 atoms, 7 bonds, 2 shapes > select up 43 atoms, 47 bonds, 2 residues, 1 model selected > select up 680 atoms, 761 bonds, 32 residues, 1 model selected > hide sel cartoons > hide sel atoms Drag select of 12 atoms, 7 bonds, 6 shapes > hide sel atoms Drag select of 3 atoms > hide sel atoms > select add #1 174751 atoms, 183003 bonds, 22 pseudobonds, 18170 residues, 3 models selected > select subtract #1 Nothing selected > select add #1 174751 atoms, 183003 bonds, 22 pseudobonds, 18170 residues, 3 models selected > show sel cartoons > select clear > select #1/N:149 10 atoms, 10 bonds, 1 residue, 1 model selected > select up 50 atoms, 51 bonds, 6 residues, 1 model selected > select up 1786 atoms, 1833 bonds, 222 residues, 1 model selected > select clear > select #5/A:6552@C42 1 atom, 1 residue, 1 model selected > select up 42 atoms, 45 bonds, 1 residue, 1 model selected > transparency sel 50 target a > color sel gray > select clear > select #1/A:2579 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 33028 atoms, 36953 bonds, 1556 residues, 1 model selected > select up 33112 atoms, 37043 bonds, 1558 residues, 1 model selected > select down 33028 atoms, 36953 bonds, 1556 residues, 1 model selected > color sel light gray > select clear > select #1/A:2610 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 33028 atoms, 36953 bonds, 1556 residues, 1 model selected > color sel light gray > lighting simple > lighting soft > select clear > lighting simple > lighting soft > lighting simple > select clear > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/RRF-2.tif > width 1201 height 757 supersample 3 transparentBackground true > select clear > select ::name=""T1C"" 210 atoms, 225 bonds, 5 residues, 3 models selected > show sel atoms > select clear > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall- > RRFbound.tif width 1201 height 757 supersample 3 transparentBackground true > lighting full > lighting simple > lighting flat > graphics silhouettes false > lighting flat > lighting simple > lighting soft > lighting flat > lighting simple > lighting soft > select #1/s:78 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 75 atoms, 74 bonds, 9 residues, 1 model selected > select up 709 atoms, 731 bonds, 87 residues, 1 model selected > color sel light sea green > select clear > select #1/s:356 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 60 atoms, 60 bonds, 8 residues, 1 model selected > select up 2446 atoms, 2508 bonds, 299 residues, 1 model selected > color sel light sea green > select clear > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall- > RRFbound.tif width 1201 height 757 supersample 3 transparentBackground true > lighting simple > lighting soft > lighting full > lighting simple > lighting flat > select protein 970185 atoms, 983997 bonds, 60 pseudobonds, 73817 residues, 11 models selected > select subtract #8 968684 atoms, 982487 bonds, 60 pseudobonds, 73624 residues, 10 models selected > cartoon style (#!1 & sel) modeHelix tube sides 20 > select clear > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall- > RRFbound-2.tif width 1201 height 757 supersample 3 transparentBackground > true > lighting flat > lighting soft > graphics silhouettes false > lighting soft > graphics silhouettes true > lighting soft > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall- > RRFbound-2.tif width 1201 height 757 supersample 3 transparentBackground > true > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/overall- > RRFbound-3.tif width 1201 height 757 supersample 3 transparentBackground > true > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > show #!7 models > hide #!7 models > save /Users/minh.duc.nguyen/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/KI/Jurkat_monosome_project/Figure/RRF1-clash/RRF.cxs 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 ATI-5.1.35 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. 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: 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: 16 GB System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0) OS Loader Version: 580~743 Software: System Software Overview: System Version: macOS 14.1.1 (23B81) Kernel Version: Darwin 23.1.0 Time since boot: 3 days, 22 hours, 42 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): 4 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 B277U: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 70.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: TDBEE003853B Mirror: Off Online: Yes Rotation: Supported Connection Type: DVI or HDMI Adapter Firmware Version: 2.4a 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-Clipper: 0.21.0 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-ISOLDE: 1.6.0 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: 2022.2.22 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 Tom Goddard all ChimeraX