id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10222 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-13.4.1-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 Current thread 0x00000001dd625e00 (most recent call first): File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 892 in init File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/__main__.py"", line 1043 in File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 87 in _run_code File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", line 197 in _run_module_as_main {""app_name"":""ChimeraX"",""timestamp"":""2023-11-24 13:33:58.00 +0100"",""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"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 13.4.1 (22F770820d)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""9DAAC893-6BE7-49DC-8E95-30E985DF105C""} { ""uptime"" : 13000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Macmini9,1"", ""coalitionID"" : 2245, ""osVersion"" : { ""train"" : ""macOS 13.4.1"", ""build"" : ""22F770820d"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2023-11-24 13:33:48.7745 +0100"", ""incident"" : ""9DAAC893-6BE7-49DC-8E95-30E985DF105C"", ""pid"" : 1829, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2023-11-24 09:59:29.7871 +0100"", ""procStartAbsTime"" : 5251742404, ""procExitAbsTime"" : 313866821997, ""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"":""85DD9DB3-7367-5375-98FC-D2F8EC814488"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""5FD5FD9B-49CD-7E8C-1EF6-0108DFBFFEA0"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 0, ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x18 is not in any region. Bytes before following region: 105554055790568\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n MALLOC_NANO (reserved) 600038000000-600040000000 [128.0M] rw-\/rwx SM=NUL ...(unallocated)"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000018"",""rawCodes"":[1,24],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000018""}, ""vmregioninfo"" : ""0x18 is not in any region. 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\nTOTAL, minus reserved VM space 4.5G 4789 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""d49a9b2a4b2f527f1be97178dc89a62dbc4752dd"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""62c73fd17cce0d1b0bcb8a02"", ""factorPackIds"" : { ""SIRI_DIALOG_ASSETS"" : ""651482b98d79034dd899e383"" }, ""deploymentId"" : 240000207 }, { ""rolloutId"" : ""6297d96be2c9387df974efa4"", ""factorPackIds"" : { }, ""deploymentId"" : 240000014 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/pdb6w0m.ent"" pdb6w0m.ent title: Human 8-oxoguanine glycosylase crosslinked with oxog lesion containing DNA [more info...] Chain information for pdb6w0m.ent #1 --- Chain | Description | UniProt A | N-glycosylase/DNA lyase | OGG1_HUMAN 12-325 B | DNA (5'-D(P*CP*GP*TP*CP*CP*ap*(8OG)P*GP*TP*CP*TP*ap*C)-3') | C | DNA (5'-D(P*GP*GP*TP*ap*GP*ap*CP*CP*TP*GP*GP*ap*CP*GP*C)- 3') | Non-standard residues in pdb6w0m.ent #1 --- 8OG — 8-oxo-2'-deoxy-guanosine-5'-monophosphate (8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-monophosphate) MG — magnesium ion S5Y — 2-(2-ethoxyethoxy)ethanethiol > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/pdb6w13.ent"" pdb6w13.ent title: Human 8-oxoguanine glycosylase interrogating fully intrahelical oxog lesion DNA [more info...] Chain information for pdb6w13.ent #2 --- Chain | Description | UniProt A | N-glycosylase/DNA lyase | OGG1_HUMAN 12-325 B | DNA (5'-D(P*CP*ap*(8OG)P*GP*TP*CP*T)-3') | C | DNA (5'-D(P*ap*CP*CP*TP*GP*G)-3') | Non-standard residues in pdb6w13.ent #2 --- 8OG — 8-oxo-2'-deoxy-guanosine-5'-monophosphate (8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-monophosphate) ACT — acetate ion MG — magnesium ion S5Y — 2-(2-ethoxyethoxy)ethanethiol > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/pdb6w0r.ent"" pdb6w0r.ent title: Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA [more info...] Chain information for pdb6w0r.ent #3 --- Chain | Description | UniProt A | N-glycosylase/DNA lyase | OGG1_HUMAN 12-323 B | DNA (5'-D(P*CP*ap*GP*GP*TP*C)-3') | C | DNA (5'-D(P*CP*CP*TP*GP*G)-3') | Non-standard residues in pdb6w0r.ent #3 --- NA — sodium ion NO3 — nitrate ion S5Y — 2-(2-ethoxyethoxy)ethanethiol > ui tool show Matchmaker > matchmaker #!1-2 to #3 ssFraction 1.0 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 1 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 pdb6w0r.ent, chain A (#3) with pdb6w0m.ent, chain A (#1), sequence alignment score = 1559 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: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 298 pruned atom pairs is 0.605 angstroms; (across all 312 pairs: 0.948) Matchmaker pdb6w0r.ent, chain A (#3) with pdb6w13.ent, chain A (#2), sequence alignment score = 1546 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: pdb6w13.ent #2/A, pdb6w0r.ent #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 282 pruned atom pairs is 0.326 angstroms; (across all 307 pairs: 1.987) > matchmaker #!1-2 to #3 ssFraction 1.0 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 1 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 pdb6w0r.ent, chain A (#3) with pdb6w0m.ent, chain A (#1), sequence alignment score = 1559 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: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 3 RMSD between 298 pruned atom pairs is 0.605 angstroms; (across all 312 pairs: 0.948) Matchmaker pdb6w0r.ent, chain A (#3) with pdb6w13.ent, chain A (#2), sequence alignment score = 1546 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: pdb6w13.ent #2/A, pdb6w0r.ent #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 4 RMSD between 282 pruned atom pairs is 0.326 angstroms; (across all 307 pairs: 1.987) > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/R154A-204A.pdb"" R154A-204A.pdb title: Esmfold V1 prediction for input [more info...] Chain information for R154A-204A.pdb #4 --- Chain | Description A | No description available Associated R154A-204A.pdb chain A to pdb6w0r.ent, chain A with 7 mismatches Chains used in RMSD evaluation for alignment 1: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A Associated R154A-204A.pdb chain A to pdb6w0r.ent, chain A with 7 mismatches Chains used in RMSD evaluation for alignment 2: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A Associated R154A-204A.pdb chain A to pdb6w0r.ent, chain A with 7 mismatches Chains used in RMSD evaluation for alignment 3: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A Associated R154A-204A.pdb chain A to pdb6w0r.ent, chain A with 7 mismatches Chains used in RMSD evaluation for alignment 4: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/N149-150A.pdb"" N149-150A.pdb title: Esmfold V1 prediction for input [more info...] Chain information for N149-150A.pdb #5 --- Chain | Description A | No description available Associated N149-150A.pdb chain A to pdb6w0r.ent, chain A with 7 mismatches Chains used in RMSD evaluation for alignment 1: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A Associated N149-150A.pdb chain A to pdb6w0r.ent, chain A with 7 mismatches Chains used in RMSD evaluation for alignment 2: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A Associated N149-150A.pdb chain A to pdb6w0r.ent, chain A with 7 mismatches Chains used in RMSD evaluation for alignment 3: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A Associated N149-150A.pdb chain A to pdb6w0r.ent, chain A with 7 mismatches Chains used in RMSD evaluation for alignment 4: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/WT.pdb"" WT.pdb title: Esmfold V1 prediction for input [more info...] Chain information for WT.pdb #6 --- Chain | Description A | No description available Associated WT.pdb chain A to pdb6w0r.ent, chain A with 5 mismatches Chains used in RMSD evaluation for alignment 1: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A Associated WT.pdb chain A to pdb6w0r.ent, chain A with 5 mismatches Chains used in RMSD evaluation for alignment 2: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A Associated WT.pdb chain A to pdb6w0r.ent, chain A with 5 mismatches Chains used in RMSD evaluation for alignment 3: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A Associated WT.pdb chain A to pdb6w0r.ent, chain A with 5 mismatches Chains used in RMSD evaluation for alignment 4: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/Y203A.pdb"" Y203A.pdb title: Esmfold V1 prediction for input [more info...] Chain information for Y203A.pdb #7 --- Chain | Description A | No description available Associated Y203A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 1: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A Associated Y203A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 2: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A Associated Y203A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 3: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A Associated Y203A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 4: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/N150A.pdb"" N150A.pdb title: Esmfold V1 prediction for input [more info...] Chain information for N150A.pdb #8 --- Chain | Description A | No description available Associated N150A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 1: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A Associated N150A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 2: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A Associated N150A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 3: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A Associated N150A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 4: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/N149A.pdb"" N149A.pdb title: Esmfold V1 prediction for input [more info...] Chain information for N149A.pdb #9 --- Chain | Description A | No description available Associated N149A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 1: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A Associated N149A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 2: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A Associated N149A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 3: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A Associated N149A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 4: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/R204A.pdb"" R204A.pdb title: Esmfold V1 prediction for input [more info...] Chain information for R204A.pdb #10 --- Chain | Description A | No description available Associated R204A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 1: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A, R204A.pdb #10/A Associated R204A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 2: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A, R204A.pdb #10/A Associated R204A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 3: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A, R204A.pdb #10/A Associated R204A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 4: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A, R204A.pdb #10/A > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/R154A.pdb"" R154A.pdb title: Esmfold V1 prediction for input [more info...] Chain information for R154A.pdb #11 --- Chain | Description A | No description available Associated R154A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 1: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A, R204A.pdb #10/A, R154A.pdb #11/A Associated R154A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 2: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A, R204A.pdb #10/A, R154A.pdb #11/A Associated R154A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 3: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A, R204A.pdb #10/A, R154A.pdb #11/A Associated R154A.pdb chain A to pdb6w0r.ent, chain A with 6 mismatches Chains used in RMSD evaluation for alignment 4: pdb6w13.ent #2/A, pdb6w0r.ent #3/A, R154A-204A.pdb #4/A, N149-150A.pdb #5/A, WT.pdb #6/A, Y203A.pdb #7/A, N150A.pdb #8/A, N149A.pdb #9/A, R204A.pdb #10/A, R154A.pdb #11/A > ui tool show Matchmaker > matchmaker #4-11#!1-2 to #3 ssFraction 1.0 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 1 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 pdb6w0r.ent, chain A (#3) with R154A-204A.pdb, chain A (#4), sequence alignment score = 1490 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: pdb6w0r.ent #3/A, R154A-204A.pdb #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 5 RMSD between 259 pruned atom pairs is 0.777 angstroms; (across all 307 pairs: 2.859) Matchmaker pdb6w0r.ent, chain A (#3) with N149-150A.pdb, chain A (#5), sequence alignment score = 1464 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: pdb6w0r.ent #3/A, N149-150A.pdb #5/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 6 RMSD between 265 pruned atom pairs is 0.747 angstroms; (across all 304 pairs: 2.909) Matchmaker pdb6w0r.ent, chain A (#3) with WT.pdb, chain A (#6), sequence alignment score = 1490 Alignment identifier is 7 Showing conservation header (""seq_conservation"" residue attribute) for alignment 7 Hiding conservation header for alignment 7 Chains used in RMSD evaluation for alignment 7: pdb6w0r.ent #3/A, WT.pdb #6/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 7 RMSD between 279 pruned atom pairs is 0.772 angstroms; (across all 308 pairs: 2.711) Matchmaker pdb6w0r.ent, chain A (#3) with Y203A.pdb, chain A (#7), sequence alignment score = 1454 Alignment identifier is 8 Showing conservation header (""seq_conservation"" residue attribute) for alignment 8 Hiding conservation header for alignment 8 Chains used in RMSD evaluation for alignment 8: pdb6w0r.ent #3/A, Y203A.pdb #7/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 8 RMSD between 275 pruned atom pairs is 0.756 angstroms; (across all 304 pairs: 2.680) Matchmaker pdb6w0r.ent, chain A (#3) with N150A.pdb, chain A (#8), sequence alignment score = 1490 Alignment identifier is 9 Showing conservation header (""seq_conservation"" residue attribute) for alignment 9 Hiding conservation header for alignment 9 Chains used in RMSD evaluation for alignment 9: pdb6w0r.ent #3/A, N150A.pdb #8/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 9 RMSD between 279 pruned atom pairs is 0.774 angstroms; (across all 308 pairs: 2.717) Matchmaker pdb6w0r.ent, chain A (#3) with N149A.pdb, chain A (#9), sequence alignment score = 1490 Alignment identifier is 10 Showing conservation header (""seq_conservation"" residue attribute) for alignment 10 Hiding conservation header for alignment 10 Chains used in RMSD evaluation for alignment 10: pdb6w0r.ent #3/A, N149A.pdb #9/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 10 RMSD between 279 pruned atom pairs is 0.781 angstroms; (across all 308 pairs: 2.725) Matchmaker pdb6w0r.ent, chain A (#3) with R204A.pdb, chain A (#10), sequence alignment score = 1490 Alignment identifier is 11 Showing conservation header (""seq_conservation"" residue attribute) for alignment 11 Hiding conservation header for alignment 11 Chains used in RMSD evaluation for alignment 11: pdb6w0r.ent #3/A, R204A.pdb #10/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 11 RMSD between 259 pruned atom pairs is 0.771 angstroms; (across all 307 pairs: 2.856) Matchmaker pdb6w0r.ent, chain A (#3) with R154A.pdb, chain A (#11), sequence alignment score = 1490 Alignment identifier is 12 Showing conservation header (""seq_conservation"" residue attribute) for alignment 12 Hiding conservation header for alignment 12 Chains used in RMSD evaluation for alignment 12: pdb6w0r.ent #3/A, R154A.pdb #11/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 12 RMSD between 277 pruned atom pairs is 0.761 angstroms; (across all 308 pairs: 2.708) Matchmaker pdb6w0r.ent, chain A (#3) with pdb6w0m.ent, chain A (#1), sequence alignment score = 1559 Alignment identifier is 13 Showing conservation header (""seq_conservation"" residue attribute) for alignment 13 Hiding conservation header for alignment 13 Chains used in RMSD evaluation for alignment 13: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 13 RMSD between 298 pruned atom pairs is 0.605 angstroms; (across all 312 pairs: 0.948) Matchmaker pdb6w0r.ent, chain A (#3) with pdb6w13.ent, chain A (#2), sequence alignment score = 1546 Alignment identifier is 14 Showing conservation header (""seq_conservation"" residue attribute) for alignment 14 Hiding conservation header for alignment 14 Chains used in RMSD evaluation for alignment 14: pdb6w13.ent #2/A, pdb6w0r.ent #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 14 RMSD between 282 pruned atom pairs is 0.326 angstroms; (across all 307 pairs: 1.987) > matchmaker #4-11#!1-2 to #3 ssFraction 1.0 showAlignment true Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 1 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 pdb6w0r.ent, chain A (#3) with R154A-204A.pdb, chain A (#4), sequence alignment score = 1490 Alignment identifier is 15 Showing conservation header (""seq_conservation"" residue attribute) for alignment 15 Hiding conservation header for alignment 15 Chains used in RMSD evaluation for alignment 15: pdb6w0r.ent #3/A, R154A-204A.pdb #4/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 15 RMSD between 259 pruned atom pairs is 0.777 angstroms; (across all 307 pairs: 2.859) Matchmaker pdb6w0r.ent, chain A (#3) with N149-150A.pdb, chain A (#5), sequence alignment score = 1464 Alignment identifier is 16 Showing conservation header (""seq_conservation"" residue attribute) for alignment 16 Hiding conservation header for alignment 16 Chains used in RMSD evaluation for alignment 16: pdb6w0r.ent #3/A, N149-150A.pdb #5/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 16 RMSD between 265 pruned atom pairs is 0.747 angstroms; (across all 304 pairs: 2.909) Matchmaker pdb6w0r.ent, chain A (#3) with WT.pdb, chain A (#6), sequence alignment score = 1490 Alignment identifier is 17 Showing conservation header (""seq_conservation"" residue attribute) for alignment 17 Hiding conservation header for alignment 17 Chains used in RMSD evaluation for alignment 17: pdb6w0r.ent #3/A, WT.pdb #6/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 17 RMSD between 279 pruned atom pairs is 0.772 angstroms; (across all 308 pairs: 2.711) Matchmaker pdb6w0r.ent, chain A (#3) with Y203A.pdb, chain A (#7), sequence alignment score = 1454 Alignment identifier is 18 Showing conservation header (""seq_conservation"" residue attribute) for alignment 18 Hiding conservation header for alignment 18 Chains used in RMSD evaluation for alignment 18: pdb6w0r.ent #3/A, Y203A.pdb #7/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 18 RMSD between 275 pruned atom pairs is 0.756 angstroms; (across all 304 pairs: 2.680) Matchmaker pdb6w0r.ent, chain A (#3) with N150A.pdb, chain A (#8), sequence alignment score = 1490 Alignment identifier is 19 Showing conservation header (""seq_conservation"" residue attribute) for alignment 19 Hiding conservation header for alignment 19 Chains used in RMSD evaluation for alignment 19: pdb6w0r.ent #3/A, N150A.pdb #8/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 19 RMSD between 279 pruned atom pairs is 0.774 angstroms; (across all 308 pairs: 2.717) Matchmaker pdb6w0r.ent, chain A (#3) with N149A.pdb, chain A (#9), sequence alignment score = 1490 Alignment identifier is 20 Showing conservation header (""seq_conservation"" residue attribute) for alignment 20 Hiding conservation header for alignment 20 Chains used in RMSD evaluation for alignment 20: pdb6w0r.ent #3/A, N149A.pdb #9/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 20 RMSD between 279 pruned atom pairs is 0.781 angstroms; (across all 308 pairs: 2.725) Matchmaker pdb6w0r.ent, chain A (#3) with R204A.pdb, chain A (#10), sequence alignment score = 1490 Alignment identifier is 21 Showing conservation header (""seq_conservation"" residue attribute) for alignment 21 Hiding conservation header for alignment 21 Chains used in RMSD evaluation for alignment 21: pdb6w0r.ent #3/A, R204A.pdb #10/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 21 RMSD between 259 pruned atom pairs is 0.771 angstroms; (across all 307 pairs: 2.856) Matchmaker pdb6w0r.ent, chain A (#3) with R154A.pdb, chain A (#11), sequence alignment score = 1490 Alignment identifier is 22 Showing conservation header (""seq_conservation"" residue attribute) for alignment 22 Hiding conservation header for alignment 22 Chains used in RMSD evaluation for alignment 22: pdb6w0r.ent #3/A, R154A.pdb #11/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 22 RMSD between 277 pruned atom pairs is 0.761 angstroms; (across all 308 pairs: 2.708) Matchmaker pdb6w0r.ent, chain A (#3) with pdb6w0m.ent, chain A (#1), sequence alignment score = 1559 Alignment identifier is 23 Showing conservation header (""seq_conservation"" residue attribute) for alignment 23 Hiding conservation header for alignment 23 Chains used in RMSD evaluation for alignment 23: pdb6w0m.ent #1/A, pdb6w0r.ent #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 23 RMSD between 298 pruned atom pairs is 0.605 angstroms; (across all 312 pairs: 0.948) Matchmaker pdb6w0r.ent, chain A (#3) with pdb6w13.ent, chain A (#2), sequence alignment score = 1546 Alignment identifier is 24 Showing conservation header (""seq_conservation"" residue attribute) for alignment 24 Hiding conservation header for alignment 24 Chains used in RMSD evaluation for alignment 24: pdb6w13.ent #2/A, pdb6w0r.ent #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 24 RMSD between 282 pruned atom pairs is 0.326 angstroms; (across all 307 pairs: 1.987) > select nucleic-acid 1067 atoms, 1190 bonds, 52 residues, 3 models selected > show sel cartoons > hide sel atoms > show sel atoms > nucleotides sel atoms > style nucleic & sel stick Changed 1067 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 1067 atom styles > select protein 29259 atoms, 30061 bonds, 3 pseudobonds, 3699 residues, 14 models selected > hide sel atoms > show sel cartoons > ui mousemode right select Drag select of 125 residues > select nucleic-acid 1067 atoms, 1190 bonds, 52 residues, 3 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #1/B Alignment identifier is 1/B > sequence chain #1/C Alignment identifier is 1/C > sequence chain #2/B Alignment identifier is 2/B > sequence chain #2/C Alignment identifier is 2/C > sequence chain #3/B Alignment identifier is 3/B > sequence chain #3/C Alignment identifier is 3/C > color #6 #f2a940ff > color #7 #2d2627ff > color #8 #e8baedff > color #9 #9ccae2ff > color #11 #6c5dcfff > color #5 #cbb797ff > color #11 #f1a192ff > color #4 #559af7ff > color #7 #f9df4fff > color #10 #d1d1d1ff Unsupported scale factor (0.000000) detected on Display0 QPainter::begin: Paint device returned engine == 0, type: 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.6.1 (2023-05-09) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/pdb6w13.ent"" pdb6w13.ent title: Human 8-oxoguanine glycosylase interrogating fully intrahelical oxog lesion DNA [more info...] Chain information for pdb6w13.ent #1 --- Chain | Description | UniProt A | N-glycosylase/DNA lyase | OGG1_HUMAN 12-325 B | DNA (5'-D(P*CP*ap*(8OG)P*GP*TP*CP*T)-3') | C | DNA (5'-D(P*ap*CP*CP*TP*GP*G)-3') | Non-standard residues in pdb6w13.ent #1 --- 8OG — 8-oxo-2'-deoxy-guanosine-5'-monophosphate (8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-monophosphate) ACT — acetate ion MG — magnesium ion S5Y — 2-(2-ethoxyethoxy)ethanethiol > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/pdb6w0r.ent"" pdb6w0r.ent title: Human 8-oxoguanine glycosylase interrogating fully intrahelical undamaged DNA [more info...] Chain information for pdb6w0r.ent #2 --- Chain | Description | UniProt A | N-glycosylase/DNA lyase | OGG1_HUMAN 12-323 B | DNA (5'-D(P*CP*ap*GP*GP*TP*C)-3') | C | DNA (5'-D(P*CP*CP*TP*GP*G)-3') | Non-standard residues in pdb6w0r.ent #2 --- NA — sodium ion NO3 — nitrate ion S5Y — 2-(2-ethoxyethoxy)ethanethiol > open ""/Users/nicolasbigot/Library/Group > Containers/G69SCX94XU.duck/Library/Application > Support/duck/Volumes.noindex/OneDrivePerso1/My Files/SP@RTE Lab > V/Experiments/Protein_structures/OGG1/pdb6w0m.ent"" pdb6w0m.ent title: Human 8-oxoguanine glycosylase crosslinked with oxog lesion containing DNA [more info...] Chain information for pdb6w0m.ent #3 --- Chain | Description | UniProt A | N-glycosylase/DNA lyase | OGG1_HUMAN 12-325 B | DNA (5'-D(P*CP*GP*TP*CP*CP*ap*(8OG)P*GP*TP*CP*TP*ap*C)-3') | C | DNA (5'-D(P*GP*GP*TP*ap*GP*ap*CP*CP*TP*GP*GP*ap*CP*GP*C)- 3') | Non-standard residues in pdb6w0m.ent #3 --- 8OG — 8-oxo-2'-deoxy-guanosine-5'-monophosphate (8-oxo-7,8-dihydro-2'-deoxy-guanosine-5'-monophosphate) MG — magnesium ion S5Y — 2-(2-ethoxyethoxy)ethanethiol OpenGL version: 4.1 Metal - 83.1 OpenGL renderer: Apple M1 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: Mac mini Model Identifier: Macmini9,1 Model Number: Z12N0000CFN/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8422.121.1 OS Loader Version: 8422.121.1 Software: System Software Overview: System Version: macOS 13.4.1 (c) (22F770820d) Kernel Version: Darwin 22.5.0 Time since boot: 4 heures et 25 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: 27 PIXEL VIEW: Resolution: 3840 x 2158 UI Looks like: 1920 x 1079 @ 75.00Hz Main Display: Yes Mirror: Off Online: Yes Rotation: Supported 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 Tom Goddard all ChimeraX