id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17228 Crashed in QTabBar::paintEvent(), QPainter::begin: Paint device returned engine == 0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-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 0x0000000339ec7000 (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 0x0000000338ebb000 (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 0x0000000337eaf000 (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 0x0000000336ea3000 (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 0x0000000335e97000 (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 0x0000000334e8b000 (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 0x0000000333e7f000 (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 0x0000000332e73000 (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 0x0000000331e67000 (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 0x0000000330e5b000 (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 0x000000032fe4f000 (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 0x000000032481f000 (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 0x0000000323813000 (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 0x00000001ff93c840 (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"":""2025-03-28 10:04:35.00 +0200"",""app_version"":""1.6.1"",""slice_uuid"":""a5992708-d5b4-36ec-ac0a-e525f6105b56"",""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 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""57C8EE20-39AD-4EDD-9AD3-7C4721295343""} { ""uptime"" : 250000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 502, ""deployVersion"" : 210, ""modelCode"" : ""Mac14,9"", ""coalitionID"" : 10461, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-03-28 10:04:17.3897 +0200"", ""codeSigningMonitor"" : 1, ""incident"" : ""57C8EE20-39AD-4EDD-9AD3-7C4721295343"", ""pid"" : 10021, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-03-22 18:21:53.8563 +0200"", ""procStartAbsTime"" : 1866520822782, ""procExitAbsTime"" : 6064418128088, ""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"":""798DEB1B-6975-57D8-A0B5-C478E0AEDC19"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""AFB027DA-CA90-91B1-5FBC-43F4DAD0B01C"", ""lowPowerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""9D809F34-B7B5-4A21-B11E-CC6770304E22"", ""wakeTime"" : 1, ""sleepWakeUUID"" : ""DD3101CD-3A4B-4EEB-9668-58D3EE68BD8C"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. Bytes before following region: 4377935848\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 104f20000-104f24000 [ 16K] r-x\/r-x SM=COW \/Applications\/ChimeraX-1.6.1.app\/Contents\/MacOS\/ChimeraX"", ""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"":10021}, ""vmregioninfo"" : ""0x18 is not in any region. 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\n__TEXT 1.3G 1157 \n__TPRO_CONST 272K 2 \ndyld private memory 256K 1 \nmapped file 637.6M 110 \nowned unmapped memory 201.0M 1 \npage table in kernel 7051K 1 \nshared memory 3184K 26 \n=========== ======= ======= \nTOTAL 23.4G 7220 \nTOTAL, minus reserved VM space 22.9G 7220 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""a337765b6da6d8feb4cf1b30ed96fc92861c360e"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""6246d6a916a70b047e454124"", ""factorPackIds"" : { }, ""deploymentId"" : 240000010 }, { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields 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/Monika/Downloads/DRT4 1.pdb"" format pdb Chain information for DRT4 1.pdb #1 --- Chain | Description A B C D E F | No description available G H I J K L | No description available > open > /Users/Monika/Documents/retrons/DRT4/structure/g_DRT4_hexa_rnp_real_space_refined_001.pdb > format pdb Chain information for g_DRT4_hexa_rnp_real_space_refined_001.pdb #2 --- Chain | Description A B C D E F | No description available G H I J K L | No description available > hide #1 models > set bgColor white > hide #2 atoms > show #2 cartoons > dssp > color #2 bynucleotide > undo Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 3 Alignment identifier is 4 > select #2/A-F:209 24 atoms, 18 bonds, 6 residues, 1 model selected > select #2/A-F:209-210 66 atoms, 66 bonds, 12 residues, 1 model selected > select > #2/A-F:6-17,41-49,82-94,96-104,128-139,153-156,159-167,169-176,187-198,211-231,249-265,287-294,306-308,312-328,334-342,351-364,366-373,376-378,386-401,404-416,423-432,435-444,448-461,464-479,491-497 13596 atoms, 13770 bonds, 1644 residues, 1 model selected > select #2/A-F:205 24 atoms, 18 bonds, 6 residues, 1 model selected > select #2/A-F:205 24 atoms, 18 bonds, 6 residues, 1 model selected Populating font family aliases took 195 ms. Replace uses of missing font family ""Times"" with one that exists to avoid this cost. > rainbow sel > select #1/A#2/A 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > undo > cartoon style sel modeHelix tube sides 20 > select #1/A#2/A 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel rebecca purple > color sel dark slate blue > color sel slate blue > color sel indigo > color sel rebecca purple > color sel dark magenta > color sel purple > color sel rebecca purple > color sel blue violet > color sel dark orchid > color sel rebecca purple > color sel blue violet > color sel rebecca purple > select #1/B#2/B 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > select #1/C#2/C 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dark violet > color sel blue violet > color sel medium orchid > color sel medium violet red > color sel dark orchid > color sel dark magenta > color sel purple > color sel medium violet red > color sel medium orchid > select #1/D#2/D 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel pale violet red > color sel thistle > color sel pale violet red > select #1/C#2/C 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel deep pink > color sel dark violet > color sel hot pink > color sel blue violet > color sel orchid > color sel medium orchid > color sel medium violet red > color sel medium orchid > color sel dark orchid > color sel medium orchid > select #1/E#2/E 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel violet > color sel light pink > color sel plum > select #1/F#2/F 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel medium purple > select #1/D#2/D 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > select #1/B#2/B 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel rebecca purple > color sel dark slate blue > color sel blue violet > ui tool show ""Color Actions"" > color sel plum > color sel violet > color sel lavender > color sel thistle > color sel orchid > color sel thistle > ui tool show ""Side View"" > graphics silhouettes true > lighting soft > lighting simple > undo > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > undo > lighting full > lighting soft > ui tool show ""Color Actions"" > color sel orchid > color sel thistle > color sel plum > color sel lavender > color sel pink > ui tool show ""Color Actions"" > color sel light coral > color sel light pink > color sel pale violet red > set bgColor black > set bgColor white > select #1/C#2/C 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel purple > color sel dark magenta > color sel dark orchid > color sel blue violet > color sel slate blue > color sel indigo > color sel medium purple > color sel medium slate blue > select #1/F#2/F 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > select #1/E#2/E 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > select #1/B#2/B 12313 atoms, 12511 bonds, 1010 residues, 2 models selected > ui tool show ""Color Actions"" > color sel plum > color sel lavender > color sel thistle > color sel light pink > select #1/G#2/G 400 atoms, 439 bonds, 15 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dark slate gray > color sel gold > color sel orange > color sel light salmon > select #1/H#2/H 400 atoms, 439 bonds, 15 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light salmon > select #1/I#2/I 400 atoms, 439 bonds, 15 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light salmon > select #1/J#2/J 400 atoms, 439 bonds, 15 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light salmon > select #1/K#2/K 400 atoms, 439 bonds, 15 residues, 2 models selected > ui tool show ""Color Actions"" > color sel dark salmon > color sel light salmon > ui tool show ""Color Actions"" > color sel light salmon > select #1/L#2/L 400 atoms, 439 bonds, 15 residues, 2 models selected > ui tool show ""Color Actions"" > color sel light salmon > deselect Unknown command: deselect > select clear > lighting soft > graphics silhouettes false > lighting full > lighting soft > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster.cxs > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_1.tif > width 936 height 768 supersample 3 > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_2.tif > width 704 height 543 supersample 3 > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_3.tif > width 920 height 723 supersample 3 > select #1/G#2/G 400 atoms, 439 bonds, 15 residues, 2 models selected > style sel & #2 stick Changed 141 atom styles > show sel & #2 atoms > hide sel & #2 cartoons > show sel & #2 atoms > style sel & #2 stick Changed 141 atom styles > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select #1/G#2/G 400 atoms, 439 bonds, 15 residues, 2 models selected > color sel & #2 byhetero > interfaces select & #2 & ~solvent Missing or invalid ""atoms"" argument: invalid atoms specifier > select #2/A-F:240 48 atoms, 42 bonds, 6 residues, 1 model selected > select #2/A-F:240-241 96 atoms, 90 bonds, 12 residues, 1 model selected > show sel atoms > style sel stick Changed 96 atom styles > color sel byhetero > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > show sel atoms > style sel stick Changed 72 atom styles > color sel byhetero > select #1/G-L:1 162 atoms, 174 bonds, 6 residues, 1 model selected > select #1/G-L:1 162 atoms, 174 bonds, 6 residues, 1 model selected > open ""/Users/Monika/Downloads/DRT4 1.pdb"" format pdb Chain information for DRT4 1.pdb #3 --- Chain | Description A B C D E F | No description available G H I J K L | No description available > hide #2 models > close #1 > hide #3 atoms > show #3 cartoons > select #2/G#3/G 400 atoms, 439 bonds, 15 residues, 2 models selected > show sel & #3 atoms > hide sel & #3 atoms > style sel & #3 stick Changed 259 atom styles > style sel & #3 stick Changed 259 atom styles > style sel & #3 stick Changed 259 atom styles > color sel & #3 byhetero > hide sel & #3 cartoons > style sel & #3 stick Changed 259 atom styles > show sel & #3 cartoons > style sel & #3 stick Changed 259 atom styles > show sel & #3 atoms > style sel & #3 stick Changed 259 atom styles > style sel & #3 stick Changed 259 atom styles > style sel & #3 stick Changed 259 atom styles > style sel & #3 stick Changed 259 atom styles > nucleotides sel & #3 atoms > style nucleic & sel & #3 stick Changed 259 atom styles > nucleotides sel & #3 atoms > style nucleic & sel & #3 stick Changed 259 atom styles > style sel & #3 ball Changed 259 atom styles > open > /Users/Monika/Downloads/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_0.json Failed opening file /Users/Monika/Downloads/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_0.json: fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_0.json does not look like Mole Online json file, does not contain Channels. > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select #2/A-F:125-126 126 atoms, 126 bonds, 12 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select #2/A-F:128-129 84 atoms, 78 bonds, 12 residues, 1 model selected > select #2/A-F:124-129 306 atoms, 306 bonds, 36 residues, 1 model selected > select add #3 50892 atoms, 51630 bonds, 3114 residues, 2 models selected > select #2/A-F:125-126 126 atoms, 126 bonds, 12 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select > #2/A-F:6-17,41-49,82-94,96-104,128-139,153-156,159-167,169-176,187-198,211-231,249-265,287-294,306-308,312-328,334-342,351-364,366-373,376-378,386-401,404-416,423-432,435-444,448-461,464-479,491-497 13596 atoms, 13770 bonds, 1644 residues, 1 model selected > select #2/A-F:125-126 126 atoms, 126 bonds, 12 residues, 1 model selected > select #2/A-F:125-126 126 atoms, 126 bonds, 12 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select > #2/A-F:6-17,41-49,82-94,96-104,128-139,153-156,159-167,169-176,187-198,211-231,249-265,287-294,306-308,312-328,334-342,351-364,366-373,376-378,386-401,404-416,423-432,435-444,448-461,464-479,491-497 13596 atoms, 13770 bonds, 1644 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select add #2 25692 atoms, 26382 bonds, 3072 residues, 1 model selected > select subtract #2 Nothing selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select add #2 25692 atoms, 26382 bonds, 3072 residues, 1 model selected > select subtract #2 Nothing selected > select > #2/A-F:6-17,41-49,82-94,96-104,128-139,153-156,159-167,169-176,187-198,211-231,249-265,287-294,306-308,312-328,334-342,351-364,366-373,376-378,386-401,404-416,423-432,435-444,448-461,464-479,491-497 13596 atoms, 13770 bonds, 1644 residues, 1 model selected > show #2 models > hide #2 models Alignment identifier is 1 > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select #2/A-F:125 72 atoms, 72 bonds, 6 residues, 1 model selected > select #2/A-F:204 60 atoms, 60 bonds, 6 residues, 1 model selected > select #2/A-F:204-206 126 atoms, 126 bonds, 18 residues, 1 model selected > select add #2 25692 atoms, 26382 bonds, 3072 residues, 1 model selected > select subtract #2 Nothing selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select :125 210 atoms, 210 bonds, 12 residues, 2 models selected > style sel & #3 stick Changed 138 atom styles > nucleotides sel & #3 atoms > style nucleic & sel & #3 stick Changed 0 atom styles > show sel & #3 atoms Alignment identifier is 1 Alignment identifier is 2 Alignment identifier is 1 Alignment identifier is 3 > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 259 atom styles > style sel stick Changed 259 atom styles > style sel ball Changed 259 atom styles > style sel sphere Changed 259 atom styles > style sel ball Changed 259 atom styles > style sel stick Changed 259 atom styles > show sel atoms > style sel stick Changed 259 atom styles > show sel atoms > hide sel cartoons > select #3/C 8172 atoms, 8271 bonds, 505 residues, 1 model selected > open > /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_1.json Failed opening file /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_1.json: fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_1.json does not look like Mole Online json file, does not contain Channels. > open > /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif Chain information for fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif #1 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . > open > /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif Chain information for fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif #4 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . > open > /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif Chain information for fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_model_0.cif #5 --- Chain | Description A B C D E F | . G H I J K L | . M N O P Q R | . > hide #3 models > hide #1 models > hide #4 models > hide #5 models > show #4 models > open > /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_4.json Failed opening file /Users/Monika/Documents/retrons/DRT4/structure/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24/fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_4.json: fold_drt4_hexamer_withlongdna_with_gp44_2025_3_24_summary_confidences_4.json does not look like Mole Online json file, does not contain Channels. > show #1 models > hide #4 models > hide #1 models > show #3 models > select :G-L 42984 atoms, 39690 bonds, 4842 residues, 5 models selected > select :.G-L Expected an objects specifier or a keyword > select :.G-L Expected an objects specifier or a keyword > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light salmon > select #3/H 259 atoms, 282 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light salmon > select #3/I 259 atoms, 282 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light salmon > select #3/J 259 atoms, 282 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light salmon > ui tool show ""Color Actions"" > color sel light salmon > select #3/L 259 atoms, 282 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light salmon > select #3/L 259 atoms, 282 bonds, 8 residues, 1 model selected > select #3/K 259 atoms, 282 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light salmon > select #3/A 8172 atoms, 8271 bonds, 505 residues, 1 model selected > close #1 > close #4 > close #5 > show #2 models > hide #3 models > select #2/A 4141 atoms, 4240 bonds, 505 residues, 1 model selected > ui tool show ""Color Actions"" > hide #2 models > show #3 models > select #3/A 8172 atoms, 8271 bonds, 505 residues, 1 model selected > ui tool show ""Color Actions"" > color sel dark violet > color sel purple > color sel rebecca purple > color sel dark slate blue > color sel dark violet > color sel blue violet > color sel dark magenta > color sel purple > color sel dark violet > select #3/B 8172 atoms, 8271 bonds, 505 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium purple > color sel midnight blue > color sel medium blue > color sel blue > color sel royal blue > color sel slate blue > color sel dark slate blue > color sel slate blue > color sel medium slate blue > select #3/C 8172 atoms, 8271 bonds, 505 residues, 1 model selected > ui tool show ""Color Actions"" > color sel pale violet red > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > cartoon style #3 modeHelix tube sides 20 > lighting soft > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > lighting soft > graphics silhouettes true > graphics silhouettes false > lighting soft > lighting full > lighting soft > show #2 models > hide #3 models > show #3 models > hide #2 models > select #3/A 8172 atoms, 8271 bonds, 505 residues, 1 model selected > ui tool show ""Color Actions"" > color sel medium purple > color sel purple > color sel rebecca purple > select #3/D 8172 atoms, 8271 bonds, 505 residues, 1 model selected > ui tool show ""Color Actions"" > color sel thistle > color sel plum > select #3/F 8172 atoms, 8271 bonds, 505 residues, 1 model selected > ui tool show ""Color Actions"" > color sel lavender > color sel plum > color sel thistle > color sel light pink > ui tool show ""Color Actions"" > color sel plum > color sel lavender > color sel thistle > color sel medium purple > color sel medium slate blue > color sel medium purple > select #3/E 8172 atoms, 8271 bonds, 505 residues, 1 model selected > ui tool show ""Color Actions"" > color sel thistle > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > hide sel atoms > show sel cartoons > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > save /Users/Monika/Desktop/image1.png supersample 3 > save /Users/Monika/Desktop/image2.png supersample 3 > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_1.tif > width 776 height 507 supersample 3 > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_2.tif > width 776 height 507 supersample 3 > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_3.tif > width 776 height 507 supersample 3 > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > show sel atoms > hide sel cartoons > style sel stick Changed 259 atom styles > style sel ball Changed 259 atom styles > style sel ball Changed 259 atom styles > style sel stick Changed 259 atom styles > color sel byhetero > select > #3/A-F:6-16,41-49,82-94,96-102,128-138,153-156,159-167,169-176,187-198,211-230,249-265,287-294,305-307,312-328,334-342,351-364,366-374,376-378,386-401,404-417,423-432,435-444,448-461,464-479,491-497 26826 atoms, 26994 bonds, 1626 residues, 1 model selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > ui mousemode right select > select add #3/A:125@O2P 1 atom, 2 bonds, 1 residue, 1 model selected > select add #3/A:357 22 atoms, 27 bonds, 2 residues, 1 model selected > select add #3/A:125@HB2 23 atoms, 31 bonds, 2 residues, 1 model selected > select #3/A:357 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #3/A:125@HD1 1 atom, 1 bond, 1 residue, 1 model selected > select add #3/A:125@HE1 2 atoms, 13 bonds, 1 residue, 1 model selected > select add #3/A:125@HB3 3 atoms, 20 bonds, 1 residue, 1 model selected > select add #3/A:125@HD2 4 atoms, 20 bonds, 1 residue, 1 model selected > select add #3/A:125@HE2 5 atoms, 20 bonds, 1 residue, 1 model selected > select add #3/A:125@HB2 6 atoms, 20 bonds, 1 residue, 1 model selected > select add #3/A:125@O2P 7 atoms, 20 bonds, 1 residue, 1 model selected > select add #3/A:125@O3P 8 atoms, 20 bonds, 1 residue, 1 model selected > color sel byhetero > select #3/A-F:240 72 atoms, 66 bonds, 6 residues, 1 model selected > select #3/A-F:240-241 144 atoms, 138 bonds, 12 residues, 1 model selected > show sel atoms > style sel stick Changed 144 atom styles > color sel byhetero > ui tool show ""Side View"" > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > show sel cartoons > show sel atoms > hide sel atoms > select clear > select #3/G:1 27 atoms, 29 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > view sel > view > ui tool show ""Side View"" > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > show sel atoms > hide sel cartoons > graphics silhouettes true > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > graphics silhouettes true > graphics silhouettes false > style sel stick Changed 259 atom styles > style sel stick Changed 259 atom styles > style sel stick Changed 259 atom styles > show sel atoms > style sel stick Changed 259 atom styles > color sel byhetero > style sel ball Changed 259 atom styles > style sel stick Changed 259 atom styles > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > show sel cartoons > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > hide sel cartoons > select down 259 atoms, 282 bonds, 8 residues, 1 model selected > view sel > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_4.tif > width 987 height 643 supersample 3 > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_4_1.tif > width 987 height 643 supersample 3 > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > hide sel atoms > show sel cartoons > select #3/A-F:125 138 atoms, 138 bonds, 6 residues, 1 model selected > hide sel atoms > show sel cartoons > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_5.tif > width 987 height 643 supersample 3 > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_fig3_6.png > width 987 height 602 supersample 3 > open > /Users/Monika/Documents/retrons/DRT4/structure/cryosparc_P12_J29_006_volume_map.mrc Opened cryosparc_P12_J29_006_volume_map.mrc as #1, grid size 400,400,400, pixel 1.1, shown at level 0.0462, step 2, values float32 > volume #1 level 0.7081 > close #1 > open > /Users/Monika/Documents/retrons/DRT4/structure/DRT4emready_P12_J29_006_volume.mrc Opened DRT4emready_P12_J29_006_volume.mrc as #1, grid size 439,439,439, pixel 1, shown at level 0.000799, step 2, values float32 > volume #1 level 1.402 > volume #1 level 4.629 > hide #3 models > volume #1 level 1.954 > hide #!1 models > show #3 models Drag select of 52 residues Drag select of 39 residues > open > /Users/Monika/Documents/retrons/DRT4/structure/cryosparc_P12_J31_005_volume_map_sharp.mrc Opened cryosparc_P12_J31_005_volume_map_sharp.mrc as #4, grid size 400,400,400, pixel 1.1, shown at level 1.05, step 2, values float32 > volume #1 level 3.568 > hide #3 models > hide #!1 models > show #!1 models > hide #!1 models > hide #!4 models > show #!1 models > volume #4 level 1.496 > hide #!4 models > volume #1 level 3.016 > select #1 3 models selected > volume #1 level 2.846 > lighting soft > show #3 models > hide #3 models > close #4 > volume #1 level 3.738 > show #2 models > volume #1 color #b2b2b268 > volume #1 color #b2b2b269 > volume #1 level 6.158 > volume #1 level 2.761 > hide #!1 models > hide #2 models > show #3 models > show #!1 models > hide #!1 models > save /Users/Monika/Documents/retrons/DRT4/structure/DRT4_poster_V2.cxs > show #!1 models > hide #3 models > volume #1 level 3.355 > volume #1 color #b2b2b2 > volume #1 level 2.124 > volume #1 level 1.147 > volume #1 level 1.19 > select add #1 4 models selected > select subtract #1 Nothing selected > volume #1 level 1.232 > show #3 models > volume #1 level 1.02 > volume #1 color #b2b2b275 > color zone #1 near #3 distance 2.5 > color zone #1 near #3 distance 3 > color zone #1 near #3 distance 3.5 > select #2/G#3/G 400 atoms, 439 bonds, 15 residues, 2 models selected > nucleotides sel & #3 atoms > style nucleic & sel & #3 stick Changed 259 atom styles > show sel & #3 atoms > hide sel & #3 atoms > show sel & #3 cartoons > color sel & #3 byhetero > color sel & #3 bychain > hide #!1 models Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 0 maps. > show #!1 models > color zone #1 near sel & #3 distance 6 > undo > hide #!1 models > ui tool show ""Color Actions"" > color sel light salmon > show #!1 models > hide #!1 models > show #!1 models > volume #1 level 1.657 > color sel & #3 bychain > hide #!1 models > select add #3 50727 atoms, 51481 bonds, 3085 residues, 2 models selected > select subtract #3 141 atoms, 157 bonds, 7 residues, 1 model selected > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > ui tool show ""Color Actions"" > color sel light salmon > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > select subtract #3 Nothing selected > show #!1 models > volume #1 step 1 > hide #3 models > hide #!1 models > show #3 models > show #2 models > hide #2 models > color #3 /g light salmon > show #!1 models > color zone #1 near #3 distance 4 > color #1 light grey > color zone #1 near #3 distance 4 > hide #3 models > show #3 models > hide #!1 models > show #3 atoms > show #!1 models > hide #3 models > volume #1 level 1.84 > volume #1 level 1.52 > show #3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > style #3 ball Changed 50586 atom styles > hide #3 models > show #3 models > hide #!1 models > select #3/A:125@CG 1 atom, 1 residue, 1 model selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > hide sel atoms > show sel atoms > select #3/A:125@CZ 1 atom, 1 residue, 1 model selected > select add #3/A:125@CA 2 atoms, 1 residue, 1 model selected > select add #3/A:125@CB 3 atoms, 1 bond, 1 residue, 1 model selected > select add #3/A:125@HB2 4 atoms, 1 bond, 1 residue, 1 model selected > select add #3/A:125@CD1 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #3/A:125@HD1 6 atoms, 4 bonds, 1 residue, 1 model selected > select add #3/A:125@CG 7 atoms, 4 bonds, 1 residue, 1 model selected > select add #3/A:125@CD2 8 atoms, 5 bonds, 1 residue, 1 model selected > select add #3/A:125@CE2 9 atoms, 7 bonds, 1 residue, 1 model selected > select add #3/A:125@HE2 10 atoms, 7 bonds, 1 residue, 1 model selected > select add #3/A:125@CE1 11 atoms, 8 bonds, 1 residue, 1 model selected > select add #3/A:125@HE1 12 atoms, 8 bonds, 1 residue, 1 model selected > select add #3/A:125@OH 13 atoms, 9 bonds, 1 residue, 1 model selected > select add #3/A:125@P 14 atoms, 10 bonds, 1 residue, 1 model selected > select add #3/A:125@O3P 15 atoms, 11 bonds, 1 residue, 1 model selected > select add #3/A:125@O2P 16 atoms, 11 bonds, 1 residue, 1 model selected > select add #3/A:125@O1P 17 atoms, 12 bonds, 1 residue, 1 model selected > color sel byhetero > color sel bychain > select add #3/A:125@HB3 18 atoms, 14 bonds, 1 residue, 1 model selected > select add #3/A:125@HD2 19 atoms, 14 bonds, 1 residue, 1 model selected > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show sel atoms > hide sel atoms > show sel atoms > show sel cartoons > show sel atoms > ui tool show ""Color Actions"" > color sel rebecca purple > show #!1 models > style sel ball Changed 19 atom styles > style sel stick Changed 19 atom styles > color sel bychain > hide #3 models > show #3 models > hide #!1 models > ui tool show ""Color Actions"" > color sel rebecca purple > style sel ball Changed 19 atom styles > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > show #!1 models > hide #!1 models > color zone #1 near #3/A PTR 125 distance 4 Expected a keyword > color zone #1 near #3/A :125 distance 4 > show #!1 models > color zone #1 near #3 distance 4 > hide #3 models Drag select of 1 DRT4emready_P12_J29_006_volume.mrc > select clear > color zone #1 near #3 distance 4.5 > color zone #1 near #3 distance 5 > color zone #1 near #3 distance 5.5 > volume #1 level 1.84 > volume #1 level 1.794 > save /Users/Monika/Documents/retrons/DRT4/structure/cryoemmap_1.tif models > #1 format imagejtiff > save /Users/Monika/Documents/retrons/DRT4/structure/cryoemmap_2.tif models > #1 format imagejtiff > show #3 models > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > style sel stick Changed 50586 atom styles > volume #1 color #d3d3d3c3 > volume #1 color #d3d3d39a > volume #1 color #d3d3d399 > volume #1 color #d3d3d396 > volume #1 color #d3d3d395 > volume #1 color #d3d3d394 > select subtract #3 Nothing selected > volume #1 level 0.652 > volume #1 color #d3d3d35c > select add #1 4 models selected > graphics silhouettes true > graphics silhouettes false > select subtract #1 Nothing selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 1 model selected > show sel cartoons > hide sel atoms > select subtract #3 Nothing selected > select #3/G 259 atoms, 282 bonds, 8 residues, 1 model selected > hide #!1 models > show sel atoms > color sel byhetero > hide sel cartoons > show #!1 models > volume #1 color #ffffff5c > volume #1 color #c3c3c35c > volume #1 color #c3c3c31b > volume #1 color #c3c3c31c > color zone #1 near #3 distance 5.5 > undo > show sel cartoons > hide sel atoms > color zone #1 near #3 distance 5.5 Drag select of 37 residues, 1 DRT4emready_P12_J29_006_volume.mrc > select add #1 570 atoms, 34 residues, 5 models selected > select add #3 50586 atoms, 51324 bonds, 3078 residues, 5 models selected > select subtract #3 4 models selected > select subtract #1 Nothing selected > color zone #1 near #3 distance 6 > color zone #1 near #3 distance 3 > color zone #1 near #3 distance 5 > color zone #1 near #3 distance 6 > volume #1 level 2.707 > volume #1 level 2.388 > volume #1 level 2.159 > volume #1 level 1.291 > hide #3 models > volume #1 level 0.9718 Drag select of 1 DRT4emready_P12_J29_006_volume.mrc > select add #1 4 models selected > select subtract #1 Nothing selected > volume #1 level 1.246 > volume #1 step 2 > volume #1 step 1 Drag select of 1 DRT4emready_P12_J29_006_volume.mrc > ui tool show ""Side View"" > select add #1 4 models selected > select subtract #1 Nothing selected > save /Users/Monika/Documents/retrons/DRT4/structure/cryoemmap_1.tif models > #1 format imagejtiff > save /Users/Monika/Documents/retrons/DRT4/structure/cryomemap.png width 987 > height 602 supersample 3 > show #3 models > hide #!1 models > show #!1 models > hide #3 models > save /Users/Monika/Documents/retrons/DRT4/structure/cryomemap2.png width 987 > height 602 supersample 3 > open > /Users/Monika/Documents/retrons/DRT4/structure/fold_2025_03_27_17_32_no_atp/fold_2025_03_27_17_32_no_atp_model_0.cif Summary of feedback from opening /Users/Monika/Documents/retrons/DRT4/structure/fold_2025_03_27_17_32_no_atp/fold_2025_03_27_17_32_no_atp_model_0.cif --- note | Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif Chain information for fold_2025_03_27_17_32_no_atp_model_0.cif #4 --- Chain | Description A B C D E F | . G H I J K L | . S T U V W X | . > hide #!1 models > color byattribute Missing or invalid ""attrName"" argument: Expected a text string > color bfactor 117018 atoms, 11040 residues, atom bfactor range 12.6 to 224 > show #4 cartoons > hide #4 atoms > color bfactor #4 40740 atoms, 4890 residues, atom bfactor range 12.6 to 96.3 > undo > alphafold Unknown command: palette alphafold > color byattributee Missing or invalid ""attrName"" argument: Expected a text string > color byattribute bfactor /A range 0,100 16735 atoms, 1550 residues, atom bfactor range 29.2 to 224 > color byattribute bfactor 117018 atoms, 11040 residues, atom bfactor range 12.6 to 224 > show #!1 models > hide #4 models > save > /Users/Monika/Documents/retrons/DRT4/structure/fold_2025_03_27_17_32_no_atp/DRT4_J29_cryoEM_map_coloured.cxs > hide #!1 models > show #4 models > ui tool show ""Color Actions"" Alignment identifier is 1 Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 5 Alignment identifier is 6 Alignment identifier is 7 Alignment identifier is 8 > close #4 > open > /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_0.cif Summary of feedback from opening /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_0.cif --- note | Fetching CCD ATP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/ATP/ATP.cif Chain information for fold_2025_03_27_17_53_6_atps_model_0.cif #4 --- Chain | Description A B C D E F | . EA FA GA HA IA JA | . G H I J K L | . > show #4 surfaces > show #!4 cartoons > hide #!4 surfaces > hide #!4 atoms > close #4 > open > /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_1.cif Chain information for fold_2025_03_27_17_53_6_atps_model_1.cif #4 --- Chain | Description A B C D E F | . EA FA GA HA IA JA | . G H I J K L | . > show #4 cartoons > hide #4 atoms > color bfactor #4 40932 atoms, 4902 residues, atom bfactor range 16 to 97.5 > color bfactor #4 40932 atoms, 4902 residues, atom bfactor range 16 to 97.5 > undo > color bfactor #4 40932 atoms, 4902 residues, atom bfactor range 16 to 97.5 > rangecolor bfactor key 100 blue 50 white 0 red Unknown command: rangecolor bfactor key 100 blue 50 white 0 red > bfactor key 100 blue 50 white 0 red Unknown command: bfactor key 100 blue 50 white 0 red > ui tool show ""Color Actions"" > undo > open > /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_2.cif Chain information for fold_2025_03_27_17_53_6_atps_model_2.cif #5 --- Chain | Description A B C D E F | . EA FA GA HA IA JA | . G H I J K L | . > hide #4 models > show #5 cartoons > hide #5 atoms > hide #5 models > close #4 > close #5 > open > /Users/Monika/Documents/retrons/DRT4/structure/AF/fold_2025_03_27_17_53_6_atps_12MG/fold_2025_03_27_17_53_6_atps_model_0.cif Chain information for fold_2025_03_27_17_53_6_atps_model_0.cif #4 --- Chain | Description A B C D E F | . EA FA GA HA IA JA | . G H I J K L | . Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle 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 - 89.3 OpenGL renderer: Apple M2 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: Mac14,9 Model Number: MPHE3ZE/A Chip: Apple M2 Pro Total Number of Cores: 10 (6 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 8 days, 22 hours, 9 minutes Graphics/Displays: Apple M2 Pro: Chipset Model: Apple M2 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: 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: 2022.2.22 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 all ChimeraX