id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 8945 Unsupported scale factor (0.000000) detected on Display0 chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.6.dev202302280423 (2023-02-28 04:23:03 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 0x000000010b01a600 (most recent call first): File ""/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 284 in event_loop File ""/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/private/var/folders/ly/rl784gts4m99xvbz9ljsqs4m0000gn/T/AppTranslocation/D7F849D8-5D91-48FD-AB47-454C2A1C1B01/d/ChimeraX_Daily.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"":""2023-05-04 11:50:40.00 +0300"",""app_version"":""1.6.0"",""slice_uuid"":""5df621ee-554e-36a8-b448-93b2334e5480"",""build_version"":""1.6.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 12.6 (21G115)"",""incident_id"":""F1D16A6C-FACA-4ED7-B015-355535795F9A"",""name"":""ChimeraX""} { ""uptime"" : 460000, ""procLaunch"" : ""2023-05-03 23:30:01.6996 +0300"", ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro15,1"", ""procStartAbsTime"" : 454720028498358, ""coalitionID"" : 62889, ""osVersion"" : { ""train"" : ""macOS 12.6"", ""build"" : ""21G115"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-05-04 11:50:27.1754 +0300"", ""incident"" : ""F1D16A6C-FACA-4ED7-B015-355535795F9A"", ""bug_type"" : ""309"", ""pid"" : 68684, ""procExitAbsTime"" : 469602173896655, ""cpuType"" : ""X86-64"", ""procName"" : ""ChimeraX"", ""procPath"" : ""\/private\/var\/folders\/*\/ChimeraX_Daily.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.6.0"",""CFBundleVersion"":""1.6.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""2AB0F2FE-1C6A-5935-909A-AC9779E4A2A1"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""D2307553-8BC8-E7BE-DF5F-47E41435EDDA"", ""wakeTime"" : 12957, ""bridgeVersion"" : {""build"":""19P6067"",""train"":""6.6""}, ""sleepWakeUUID"" : ""6BADE49B-B0C3-47E8-948E-15EE51DC2BE1"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. Bytes before following region: 140737487564776\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n VM_ALLOCATE 7ffffff3f000-7ffffff40000 [ 4K] r-x\/r-x SM=ALI "", ""isCorpse"" : 1, ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""ktriageinfo"" : ""VM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\nVM - Fault hit memory shortage\n"", ""vmregioninfo"" : ""0x18 is not in any region. 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""libopenblas64_.0.dylib"" } ], ""sharedCache"" : { ""base"" : 140703262035968, ""size"" : 19331678208, ""uuid"" : ""73669942-bd8a-3e40-951f-7fbe07b51cb8"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=1.7G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=1.7G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 2048K 16 \nActivity Tracing 256K 1 \nCG backing stores 17.1M 13 \nCG image 1408K 116 \nColorSync 232K 28 \nCoreAnimation 3776K 177 \nCoreGraphics 16K 3 \nCoreServices 624K 2 \nCoreUI image data 5232K 55 \nFoundation 36K 2 \nIOKit 23.3M 3 \nKernel Alloc Once 8K 1 \nMALLOC 1.0G 1482 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 256.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 160K 40 \nStack 163.3M 41 \nStack Guard 56.0M 1 \nVM_ALLOCATE 228.6M 249 \nVM_ALLOCATE (reserved) 32.0M 1 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 59.8M 776 \n__DATA_CONST 33.0M 352 \n__DATA_DIRTY 1659K 218 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 686.1M 222 \n__TEXT 861.4M 758 \n__UNICODE 592K 1 \ndyld private memory 1056K 3 \nmapped file 572.1M 98 \nshared memory 3508K 31 \n=========== ======= ======= \nTOTAL 4.0G 4710 \nTOTAL, minus reserved VM space 3.7G 4710 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""61301e3a61217b3110231469"", ""factorPackIds"" : { ""SIRI_FIND_MY_CONFIGURATION_FILES"" : ""6348493aa52bb16adc4e4d06"" }, ""deploymentId"" : 240000023 }, { ""rolloutId"" : ""63582c5f8a53461413999550"", ""factorPackIds"" : { }, ""deploymentId"" : 240000002 } ], ""experiments"" : [ { ""treatmentId"" : ""c28e4ee6-1b08-4f90-8e05-2809e78310a3"", ""experimentId"" : ""6317d2003d24842ff850182a"", ""deploymentId"" : 400000012 }, { ""treatmentId"" : ""6dd670af-0633-45e4-ae5f-122ae4df02be"", ""experimentId"" : ""64406ba83deb637ac8a04419"", ""deploymentId"" : 900000005 } ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.dev202302280423 (2023-02-28) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Lucia/Downloads/AF-Q5JIZ5-F1-model_v4.pdb AF-Q5JIZ5-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for subtilisin-like serine protease (Q5JIZ5) [more info...] Chain information for AF-Q5JIZ5-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | subtilisin-like serine protease | TKSP_THEKO 1-663 > open /Users/Lucia/Downloads/AF-B0FXD9-F1-model_v4.pdb AF-B0FXD9-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for APRX (B0FXD9) [more info...] Chain information for AF-B0FXD9-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | APRX | B0FXD9_PSEFL 1-477 > open /Users/Lucia/Downloads/AF-B0FXE0-F1-model_v4.pdb AF-B0FXE0-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for APRX (B0FXE0) [more info...] Chain information for AF-B0FXE0-F1-model_v4.pdb #3 --- Chain | Description | UniProt A | APRX | B0FXE0_PSEFL 1-482 > view > ui tool show Matchmaker > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6 RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs: 0.851) > hide #1 models > undo > hide #1 models > undo > hide #1 models > ui tool show Matchmaker > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6 RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs: 0.851) > ui tool show ""Blast Protein"" > ui tool show Matchmaker > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6 RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs: 0.851) > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6 RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs: 0.851) > select #1/A 5014 atoms, 5135 bonds, 663 residues, 1 model selected > view > select #2/A#3/A 7039 atoms, 7182 bonds, 959 residues, 2 models selected > cartoon hide sel > undo > show #1 models > hide #1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > select #2/A 3489 atoms, 3560 bonds, 477 residues, 1 model selected > select #2/A#3/A 7039 atoms, 7182 bonds, 959 residues, 2 models selected > select #2/A#3/A 7039 atoms, 7182 bonds, 959 residues, 2 models selected > undo > hide #1 models > undo > hide #1 models > hide #2 models > show #2 models > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > undo > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > preset ""overall look"" ""publication 2 (depth-cued)"" Using preset: Overall Look / Publication 2 (Depth-Cued) Preset expands to these ChimeraX commands: set bg white graphics silhouettes f lighting depthCue t > undo > set bgColor black > select clear > ui tool show ""Modeller Comparative"" > ui tool show ""Blast Protein"" > ui tool show ""Model Loops"" No alignments chosen for modeling > ui tool show ""Model Loops"" > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > sequence chain #3/A Alignment identifier is 3/A Cannot run BLAST without some kind of sequence. > ui mousemode right ""translate selected models"" > ui mousemode right zoom > ui mousemode right ""translate selected models"" > ui mousemode right zoom > ui mousemode right ""move picked models"" > view > hide #2 models > show #2 models > hide #2 models > show #2 models > select add #2 3489 atoms, 3560 bonds, 477 residues, 1 model selected > select subtract #2 Nothing selected > select add #2 3489 atoms, 3560 bonds, 477 residues, 1 model selected > select add #3 7039 atoms, 7182 bonds, 959 residues, 2 models selected > select sequence #@ Nothing selected > select sequence #2 Nothing selected > show sequence Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show sequence #2 Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > sequence chain #3/A Alignment identifier is 3/A > view > select > #3/A:17-26,45-53,80-86,96-112,172-174,181-194,211-213,231-234,252-262,397-399,421-424,477-479 685 atoms, 685 bonds, 88 residues, 1 model selected > select > #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467 680 atoms, 679 bonds, 84 residues, 1 model selected > select #2/A:360-395 242 atoms, 246 bonds, 36 residues, 1 model selected > select #2/A:360-395 242 atoms, 246 bonds, 36 residues, 1 model selected > select > #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474 676 atoms, 675 bonds, 88 residues, 1 model selected > select > #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467 680 atoms, 679 bonds, 84 residues, 1 model selected > select > #3/A:68-74,115-119,126-133,142-144,161-165,274-276,297-299,307-309,318-320,336-338,346-348,355-357,364-366,373-375,382-384,391-393,406-408,417-419,441-447,452-458,467-472 709 atoms, 708 bonds, 87 residues, 1 model selected > select #2/A:360-395 242 atoms, 246 bonds, 36 residues, 1 model selected > select > #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474 676 atoms, 675 bonds, 88 residues, 1 model selected > select > #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467 680 atoms, 679 bonds, 84 residues, 1 model selected > select #2/A:360-395 242 atoms, 246 bonds, 36 residues, 1 model selected > select > #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474 676 atoms, 675 bonds, 88 residues, 1 model selected > select > #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467 680 atoms, 679 bonds, 84 residues, 1 model selected > select > #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474 676 atoms, 675 bonds, 88 residues, 1 model selected > select > #3/A:17-26,45-53,80-86,96-112,172-174,181-194,211-213,231-234,252-262,397-399,421-424,477-479 685 atoms, 685 bonds, 88 residues, 1 model selected > select #3/A:10-11 13 atoms, 12 bonds, 2 residues, 1 model selected > select #3/A:1-11 82 atoms, 81 bonds, 11 residues, 1 model selected > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-17 119 atoms, 118 bonds, 17 residues, 1 model selected > select #3/A:1-11 82 atoms, 81 bonds, 11 residues, 1 model selected > select #3/A:11 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/A:1-11 82 atoms, 81 bonds, 11 residues, 1 model selected > select #2/A:16-17 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:1-17 119 atoms, 118 bonds, 17 residues, 1 model selected > select > #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474 676 atoms, 675 bonds, 88 residues, 1 model selected > select > #3/A:68-74,115-119,126-133,142-144,161-165,274-276,297-299,307-309,318-320,336-338,346-348,355-357,364-366,373-375,382-384,391-393,406-408,417-419,441-447,452-458,467-472 709 atoms, 708 bonds, 87 residues, 1 model selected > select > #3/A:17-26,45-53,80-86,96-112,172-174,181-194,211-213,231-234,252-262,397-399,421-424,477-479 685 atoms, 685 bonds, 88 residues, 1 model selected > select > #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467 680 atoms, 679 bonds, 84 residues, 1 model selected > select > #2/A:17-26,45-52,80-86,96-110,167-169,176-189,206-208,226-229,247-257,279-281,392-394,416-419,472-474 676 atoms, 675 bonds, 88 residues, 1 model selected > select > #2/A:68-74,115-119,126-133,142-144,156-160,269-271,292-294,302-304,313-315,331-333,341-343,350-352,359-361,368-370,377-379,386-388,412-414,436-442,447-453,462-467 680 atoms, 679 bonds, 84 residues, 1 model selected > select > #3/A:68-74,115-119,126-133,142-144,161-165,274-276,297-299,307-309,318-320,336-338,346-348,355-357,364-366,373-375,382-384,391-393,406-408,417-419,441-447,452-458,467-472 709 atoms, 708 bonds, 87 residues, 1 model selected > select > #3/A:17-26,45-53,80-86,96-112,172-174,181-194,211-213,231-234,252-262,397-399,421-424,477-479 685 atoms, 685 bonds, 88 residues, 1 model selected > view > select #2/A:473 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:456-473 121 atoms, 122 bonds, 18 residues, 1 model selected > select #2/A:457 10 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:457-477 146 atoms, 147 bonds, 21 residues, 1 model selected > select #2/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:1-20 142 atoms, 142 bonds, 20 residues, 1 model selected > select #2/A:476-477 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:464-477 93 atoms, 92 bonds, 14 residues, 1 model selected > ui tool show ""Color Key"" > ui mousemode right ""color key"" > ui mousemode right ""move picked models"" > undo > ui tool show ""Color Key"" > ui mousemode right ""color key"" > key pos 0.69000,0.08000 > key pos 0.68000,0.08000 > key pos 0.67000,0.08000 > key pos 0.66000,0.08000 > key pos 0.65000,0.08000 > key pos 0.64000,0.08000 > key pos 0.65000,0.08000 > key pos 0.66000,0.08000 > key pos 0.67000,0.08000 > key pos 0.68000,0.08000 > key pos 0.69000,0.08000 > key pos 0.70000,0.08000 > key pos 0.71000,0.08000 > key pos 0.70000,0.08000 > key pos 0.69000,0.08000 > key pos 0.68000,0.08000 > key pos 0.67000,0.08000 > key pos 0.66000,0.08000 > key pos 0.64000,0.08000 > key pos 0.63000,0.08000 > key pos 0.62000,0.08000 > key pos 0.61000,0.08000 > key pos 0.60000,0.08000 > key pos 0.59000,0.08000 > key pos 0.58000,0.08000 > key pos 0.57000,0.08000 > key pos 0.56000,0.08000 > key pos 0.55000,0.08000 > key pos 0.54000,0.08000 > key pos 0.53000,0.08000 > key pos 0.52000,0.08000 > key pos 0.51000,0.08000 > key pos 0.50000,0.08000 > key pos 0.49000,0.08000 > key pos 0.48000,0.08000 > key pos 0.47000,0.08000 > key pos 0.46000,0.08000 > ui mousemode right ""move picked models"" > ui mousemode right ""color key"" > key delete > ui mousemode right ""move picked models"" > ui tool show ""Color Actions"" > color sel orange > color sel byelement > color sel byhetero > select #2/A:464-477 93 atoms, 92 bonds, 14 residues, 1 model selected > select add #2/A#3/A 7039 atoms, 7182 bonds, 959 residues, 2 models selected > select add #2/A#3/A 7039 atoms, 7182 bonds, 959 residues, 2 models selected > select sequence #2 Nothing selected > ui windowfill toggle > undo > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A Alignment identifier is 1/A > sequence chain #2/A Destroying pre-existing alignment with identifier 2/A Alignment identifier is 2/A > sequence chain #3/A Destroying pre-existing alignment with identifier 3/A Alignment identifier is 3/A > show #1 models > ui tool show Matchmaker > matchmaker #1,3 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs: 28.210) Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: AF-B0FXD9-F1-model_v4.pdb #2/A, AF-B0FXE0-F1-model_v4.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs: 0.851) > matchmaker #1,3 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6 Alignment identifier is 3 Showing conservation header (""seq_conservation"" residue attribute) for alignment 3 Hiding conservation header for alignment 3 Chains used in RMSD evaluation for alignment 3: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3 RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs: 28.210) Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 2178.6 Alignment identifier is 4 Showing conservation header (""seq_conservation"" residue attribute) for alignment 4 Hiding conservation header for alignment 4 Chains used in RMSD evaluation for alignment 4: AF-B0FXD9-F1-model_v4.pdb #2/A, AF-B0FXE0-F1-model_v4.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 4 RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs: 0.851) > hide #2 models > show #2 models > hide #3 models > view > select #1/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:1-13 100 atoms, 101 bonds, 13 residues, 1 model selected > select #2/A:302 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:302-304 23 atoms, 22 bonds, 3 residues, 1 model selected > hide #1 models > show #3 models > select #2/A:2-10 68 atoms, 67 bonds, 9 residues, 1 model selected > select #2/A:1-10 76 atoms, 75 bonds, 10 residues, 1 model selected > select #3/A:11 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/A:11-37 200 atoms, 203 bonds, 27 residues, 1 model selected > select #3/A:2 6 atoms, 5 bonds, 1 residue, 1 model selected > select #3/A:2-11 74 atoms, 73 bonds, 10 residues, 1 model selected > select #2/A:149-150 11 atoms, 10 bonds, 2 residues, 1 model selected > select #2/A:149-150 11 atoms, 10 bonds, 2 residues, 1 model selected > select #3/A:1 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:1-10 76 atoms, 75 bonds, 10 residues, 1 model selected > select #2/A:197 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/A:187-197 83 atoms, 86 bonds, 11 residues, 1 model selected > select #2/A:11-148,152-477 #3/A:11-148,157-482 6803 atoms, 6942 bonds, 928 residues, 2 models selected > select #2/A:62-63 19 atoms, 19 bonds, 2 residues, 1 model selected > select #2/A:62-63 19 atoms, 19 bonds, 2 residues, 1 model selected > select #2/A:65 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:65-69 37 atoms, 36 bonds, 5 residues, 1 model selected > select #2/A:11 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:11-14 25 atoms, 24 bonds, 4 residues, 1 model selected > select #2/A:11-148,152-477 #3/A:11-148,157-482 6803 atoms, 6942 bonds, 928 residues, 2 models selected > select #2/A:12-13 10 atoms, 9 bonds, 2 residues, 1 model selected > select #2/A:12-16 30 atoms, 29 bonds, 5 residues, 1 model selected > select #2/A:7 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:6-7 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:10 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:2-10 68 atoms, 67 bonds, 9 residues, 1 model selected > mattch #2 to #3 Unknown command: mattch #2 to #3 > matchmaker #2 to #3 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXE0-F1-model_v4.pdb, chain A (#3) with AF-B0FXD9-F1-model_v4.pdb, chain A (#2), sequence alignment score = 2178.6 RMSD between 464 pruned atom pairs is 0.254 angstroms; (across all 477 pairs: 0.851) > view matrix models > #2,1,-2.0327e-17,-2.0611e-19,-0.0091452,2.0327e-17,1,1.4021e-17,0.0038494,2.0611e-19,-1.4021e-17,1,0.00027844 > select add #2/A:11 #3/A:11 80 atoms, 77 bonds, 11 residues, 2 models selected > select #2/A:11 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:11-13 16 atoms, 15 bonds, 3 residues, 1 model selected > select #2/A:10-11 13 atoms, 12 bonds, 2 residues, 1 model selected > select #2/A:10-12 18 atoms, 17 bonds, 3 residues, 1 model selected > unselect Unknown command: unselect > select up 112 atoms, 111 bonds, 16 residues, 1 model selected > select up 3489 atoms, 3560 bonds, 477 residues, 1 model selected > select down 112 atoms, 111 bonds, 16 residues, 1 model selected > select down 18 atoms, 17 bonds, 3 residues, 1 model selected > select down 18 atoms, 17 bonds, 3 residues, 1 model selected > select down 18 atoms, 17 bonds, 3 residues, 1 model selected > select down 18 atoms, 17 bonds, 3 residues, 1 model selected > select down 18 atoms, 17 bonds, 3 residues, 1 model selected > select #3/A:9 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:9 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #3 models > show #3 models > select #3/A:8 5 atoms, 4 bonds, 1 residue, 1 model selected > select #3/A:3-8 47 atoms, 46 bonds, 6 residues, 1 model selected > select up 112 atoms, 111 bonds, 16 residues, 1 model selected > select #2/A:5-6 17 atoms, 16 bonds, 2 residues, 1 model selected > select #2/A:2-6 39 atoms, 38 bonds, 5 residues, 1 model selected > select #2/A:4 #3/A:4 14 atoms, 12 bonds, 2 residues, 2 models selected > select #2/A:4 #3/A:4 14 atoms, 12 bonds, 2 residues, 2 models selected MatchMaker Alignment [ID: 4] region AF-B0FXD9-F1-model_v4.pdb, chain A..AF-B0FXE0-F1-model_v4.pdb, chain A [4] RMSD: 5.181 > select #3/A:4 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:4 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #2/A:24 #3/A:24 19 atoms, 16 bonds, 3 residues, 2 models selected > select #2/A:2-6 39 atoms, 38 bonds, 5 residues, 1 model selected > deselct Unknown command: deselct > select #1/A:38-39 20 atoms, 20 bonds, 2 residues, 1 model selected > select #1/A:36-39 38 atoms, 38 bonds, 4 residues, 1 model selected > view > color #3 #e1d261ff > color #3 #345ee1ff > color #2 #ec67ccff > color #2 #ec97dbff > save /Users/Lucia/Downloads/B0FXE0_B0FXD9.gif width 1262 height 1136 > supersample 3 > preset ""initial styles"" sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > undo > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > preset ""molecular surfaces"" ""ghostly white"" Using preset: Molecular Surfaces / Ghostly White Changed 0 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color white targ s trans 80 > undo > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""overall look"" ""publication 1 (silhouettes)"" Using preset: Overall Look / Publication 1 (Silhouettes) > set bgColor #ffffff00 Preset expands to these ChimeraX commands: set bg white graphics silhouettes t lighting depthCue f > color #2 #4c65ecff > show #!1 models > hide #!3 models > hide #!1 models > show #!3 models > sym #1 copies true AF-Q5JIZ5-F1-model_v4.pdb mmCIF Assemblies --- > save /Users/Lucia/Downloads/B0FXD9(blue)_BOFXEO(pink).jpg width 1262 height > 1136 supersample 3 > sym #2 copies true AF-B0FXD9-F1-model_v4.pdb mmCIF Assemblies --- > close #2 > undo > open /Users/Lucia/Downloads/AF-B0FXD9-F1-model_v4.pdb AF-B0FXD9-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for APRX (B0FXD9) [more info...] Chain information for AF-B0FXD9-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | APRX | B0FXD9_PSEFL 1-477 Associated AF-B0FXD9-F1-model_v4.pdb chain A to AF-B0FXD9-F1-model_v4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 1: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Associated AF-B0FXD9-F1-model_v4.pdb chain A to AF-B0FXD9-F1-model_v4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 2: AF-B0FXD9-F1-model_v4.pdb #2/A, AF-B0FXE0-F1-model_v4.pdb #3/A Associated AF-B0FXD9-F1-model_v4.pdb chain A to AF-B0FXD9-F1-model_v4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 3: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Associated AF-B0FXD9-F1-model_v4.pdb chain A to AF-B0FXD9-F1-model_v4.pdb, chain A with 0 mismatches Chains used in RMSD evaluation for alignment 4: AF-B0FXD9-F1-model_v4.pdb #2/A, AF-B0FXE0-F1-model_v4.pdb #3/A > hide #!1 models > zoom 1.1 > turn 180 Expected an axis vector or a keyword > zoom 1.1 > turn 180 Expected an axis vector or a keyword > save /Users/Lucia/Downloads/B0FXD9(blue)_BOFXEO(pink)_2.jpg width 1262 > height 1136 supersample 3 > surf/a Unknown command: surf/a > lighiting gentle Unknown command: lighiting gentle > lighting shadows true > lighting shadows false > lighting flat > lighting shadows true intensity 0.5 > lighting full > lighting soft > lighting simple > preset ""initial styles"" ""space-filling (chain colors)"" Using preset: Initial Styles / Space-Filling (Chain Colors) Preset implemented in Python; no expansion to individual ChimeraX commands available. > color #2 #e961ebff > color #3 #8d86ebff > color #3 #3568ebff > color #3 #3567ebff > preset ""initial styles"" ""space-filling (single color)"" Using preset: Initial Styles / Space-Filling (Single Color) Preset implemented in Python; no expansion to individual ChimeraX commands available. > rainbow paleete PuBu-5 Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword > rainbow paleete PuBu-5 to #2 Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword > hide #2 models > rainbow paleete PuBu-5 Expected one of 'chains', 'polymers', 'residues', or 'structures' or a keyword > show #2 models > preset ""molecular surfaces"" ""atomic coloring (transparent)"" Using preset: Molecular Surfaces / Atomic Coloring (Transparent) Changed 12053 atom styles Preset expands to these ChimeraX commands: style (protein|nucleic|solvent) & @@draw_mode=0 stick surface color fromatoms targ s trans 70 > preset ""initial styles"" sticks Using preset: Initial Styles / Sticks Preset implemented in Python; no expansion to individual ChimeraX commands available. > preset ""initial styles"" cartoon Using preset: Initial Styles / Cartoon Preset implemented in Python; no expansion to individual ChimeraX commands available. > select #3/A:149-150 15 atoms, 14 bonds, 2 residues, 1 model selected > select #3/A:149-156 68 atoms, 69 bonds, 8 residues, 1 model selected > select #2/A:149 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:149-151 16 atoms, 15 bonds, 3 residues, 1 model selected > select #2/A:7 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:7-10 29 atoms, 28 bonds, 4 residues, 1 model selected > select #2/A:149-150 11 atoms, 10 bonds, 2 residues, 1 model selected > select #2/A:149-150 11 atoms, 10 bonds, 2 residues, 1 model selected > select #2/A:7 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:7-10 29 atoms, 28 bonds, 4 residues, 1 model selected > select #2/A:150 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:150 4 atoms, 3 bonds, 1 residue, 1 model selected > select #2/A:7 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:7-10 29 atoms, 28 bonds, 4 residues, 1 model selected > select #2/A:149-150 11 atoms, 10 bonds, 2 residues, 1 model selected > select #2/A:149-151 16 atoms, 15 bonds, 3 residues, 1 model selected > select #2/A:7 9 atoms, 8 bonds, 1 residue, 1 model selected > select #2/A:7-10 29 atoms, 28 bonds, 4 residues, 1 model selected > select #2/A:7-10,133-148 138 atoms, 140 bonds, 20 residues, 1 model selected > select #2/A:11-148,152-477 #3/A:11-148,157-482 6803 atoms, 6942 bonds, 928 residues, 2 models selected > undo > select #2/A:133 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/A:133-147 105 atoms, 108 bonds, 15 residues, 1 model selected > select #2/A:133 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/A:133-139 47 atoms, 47 bonds, 7 residues, 1 model selected > select add #2/A:137 #3/A:137 56 atoms, 55 bonds, 8 residues, 3 models selected > select #2/A:7-8 14 atoms, 13 bonds, 2 residues, 1 model selected > select #2/A:7-10 29 atoms, 28 bonds, 4 residues, 1 model selected > select #2/A:7-10,149-151 45 atoms, 43 bonds, 7 residues, 1 model selected > color (#!2 & sel) red > save /Users/Lucia/Downloads/B0FXD9(blue)_BOFXEO(pink)_2_selecttion(red).jpg > width 1262 height 1136 supersample 3 > hide #!3 models > show #!1 models > show #!3 models > hide #!3 models > ui tool show Matchmaker > matchmaker #!1 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs: 28.210) > ui tool show Matchmaker > matchmaker #!1 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6 Alignment identifier is 5 Showing conservation header (""seq_conservation"" residue attribute) for alignment 5 Hiding conservation header for alignment 5 Chains used in RMSD evaluation for alignment 5: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 5 RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs: 28.210) > matchmaker #!1 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6 Alignment identifier is 6 Showing conservation header (""seq_conservation"" residue attribute) for alignment 6 Hiding conservation header for alignment 6 Chains used in RMSD evaluation for alignment 6: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 6 RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs: 28.210) > ui tool show Matchmaker > matchmaker #!1 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs: 28.210) > matchmaker #!1 to #2 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-B0FXD9-F1-model_v4.pdb, chain A (#2) with AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1), sequence alignment score = 108.6 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs: 28.210) > select #2/A:454 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:454 #1/A:465 19 atoms, 18 bonds, 2 residues, 2 models selected MatchMaker Alignment [ID: 2] region AF-B0FXD9-F1-model_v4.pdb, chain A..AF-Q5JIZ5-F1-model_v4.pdb, chain A [549] RMSD: 0.637 > select #2/A:455 6 atoms, 5 bonds, 1 residue, 1 model selected > select #2/A:455-458 24 atoms, 24 bonds, 4 residues, 1 model selected > select #2/A:454 11 atoms, 11 bonds, 1 residue, 1 model selected > select #2/A:454 #1/A:465 19 atoms, 18 bonds, 2 residues, 2 models selected MatchMaker Alignment [ID: 2] region AF-B0FXD9-F1-model_v4.pdb, chain A..AF-Q5JIZ5-F1-model_v4.pdb, chain A [549] RMSD: 0.637 > select #2/A:455-456 10 atoms, 9 bonds, 2 residues, 1 model selected > select #2/A:455-458 24 atoms, 24 bonds, 4 residues, 1 model selected > select #1/A:466 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:466-469 19 atoms, 18 bonds, 4 residues, 1 model selected > select #2/A:419 7 atoms, 6 bonds, 1 residue, 1 model selected > select #2/A:419-424 37 atoms, 36 bonds, 6 residues, 1 model selected > select #2/A:453 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:453-455 25 atoms, 25 bonds, 3 residues, 1 model selected > ui tool show Matchmaker > matchmaker #!2-3 to #1 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1) with AF-B0FXD9-F1-model_v4.pdb, chain A (#2), sequence alignment score = 108.6 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXD9-F1-model_v4.pdb #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 6 pruned atom pairs is 1.137 angstroms; (across all 385 pairs: 28.210) Matchmaker AF-Q5JIZ5-F1-model_v4.pdb, chain A (#1) with AF-B0FXE0-F1-model_v4.pdb, chain A (#3), sequence alignment score = 100 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: AF-Q5JIZ5-F1-model_v4.pdb #1/A, AF-B0FXE0-F1-model_v4.pdb #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 7 pruned atom pairs is 1.061 angstroms; (across all 398 pairs: 29.294) > show #!3 models > hide #!2 models > select #3/A:29-30 20 atoms, 20 bonds, 2 residues, 1 model selected > select #3/A:29 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:256 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:256-264 74 atoms, 74 bonds, 9 residues, 1 model selected 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.dev202302280423 (2023-02-28) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-4.8.101 OpenGL renderer: AMD Radeon Pro 555X 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: 6.4.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro15,1 Processor Name: 6-Core Intel Core i7 Processor Speed: 2.2 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.140.2.0.0 (iBridge: 19.16.16067.0.0,0) OS Loader Version: 540.120.3~22 Software: System Software Overview: System Version: macOS 12.6 (21G115) Kernel Version: Darwin 21.6.0 Time since boot: 34 days 55 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: 0x0000 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Radeon Pro 555X: Chipset Model: Radeon Pro 555X Type: GPU Bus: PCIe PCIe Lane Width: x8 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x67ef Revision ID: 0x00e3 ROM Revision: 113-C980AL-075 VBIOS Version: 113-C97501P-005 EFI Driver Version: 01.A1.075 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2880 x 1800 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.0 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: 3.0.1 ChimeraX-AddCharge: 1.5.8 ChimeraX-AddH: 2.2.3 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.3.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.3 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.43.8 ChimeraX-AtomicLibrary: 10.0.5 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: 1.2.1 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.dev202302280423 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: 1.1 ChimeraX-DistMonitor: 1.3.3 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-ExperimentalCommands: 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: 2.0.11 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: 1.5.8 ChimeraX-ModelPanel: 1.3.6 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-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.6.13 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: 1.0 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: 1.10.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.1 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: 1.27.3 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: 0.1.2 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.6 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.38.0 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: 6.0.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.4 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.2.0 jupyterlab-widgets: 3.0.5 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 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 pandas: 1.5.3 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: 3.0.0 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 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: 6.4.2 PyQt6-sip: 13.4.1 PyQt6-WebEngine-commercial: 6.4.0 PyQt6-WebEngine-Qt6: 6.4.2 python-dateutil: 2.8.2 pytz: 2022.7.1 pyzmq: 25.0.0 qtconsole: 5.4.0 QtPy: 2.3.0 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 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: 1.0.2 tifffile: 2022.10.10 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.2 traitlets: 5.9.0 typing-extensions: 4.5.0 urllib3: 1.26.14 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.5 zipp: 3.15.0 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX