id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15473 Crash during screen removal chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-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 0x00000001e5f1d300 (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/save_command/dialog.py"", line 39 in display File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py"", line 127 in show_save_file_dialog File ""/Applications/ChimeraX-1.6.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/save_command/dialog.py"", line 116 in 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"":""2024-06-20 17:55:22.00 -0600"",""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 14.0 (23A344)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""BB1B339C-26A5-4E2F-80DB-0F8DA0EDE983""} { ""uptime"" : 350000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro17,1"", ""coalitionID"" : 5493, ""osVersion"" : { ""train"" : ""macOS 14.0"", ""build"" : ""23A344"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-06-20 17:54:40.8986 -0600"", ""codeSigningMonitor"" : 1, ""incident"" : ""BB1B339C-26A5-4E2F-80DB-0F8DA0EDE983"", ""pid"" : 50887, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-06-19 13:25:34.2006 -0600"", ""procStartAbsTime"" : 7517059129763, ""procExitAbsTime"" : 8617906560807, ""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"":""137D9DDF-D96F-5056-A285-A44D230577EE"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""43CEB50D-8E40-87B1-DC8B-A0FC95EA9B4F"", ""lowPowerMode"" : 1, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRXOD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVHg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""wakeTime"" : 7923, ""sleepWakeUUID"" : ""DB1733C3-DC2F-4A31-86AB-5D426728D378"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x24 is not in any region. 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""662152ede2d11d1408c4db33"", ""deploymentId"" : 400000015 } ] } } ===== Log before crash start ===== 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 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/paper.drafts/integration_paper_2/draft_20240525/supp.figure/SX.Ecoli.Cas12/ecoli-1E-pseudomonas-1F-comparison.cxs > format session opened ChimeraX session > show #!2 models > show #!5 models > show #!6 models > show #!7 models > hide #!6 models > hide #!5 models > hide #!7 models > select add #2 69728 atoms, 71070 bonds, 231 pseudobonds, 5105 residues, 4 models selected > select subtract #2 15523 atoms, 16255 bonds, 231 pseudobonds, 1657 residues, 3 models selected > select add #7 15523 atoms, 16255 bonds, 231 pseudobonds, 1657 residues, 3 models selected > select subtract #7 Nothing selected > tile 2 models tiled > select add #2 54205 atoms, 54815 bonds, 3448 residues, 1 model selected > show #!7 models > select subtract #2 6 models selected > open 7ei1 Summary of feedback from opening 7ei1 fetched from pdb --- warnings | Atom H1 is not in the residue template for MET /Q:1 Atom H1 is not in the residue template for MET /R:1 Atom H1 is not in the residue template for MET /S:1 Atom H1 is not in the residue template for MET /T:1 Atom H1 is not in the residue template for MET /U:1 3 messages similar to the above omitted note | Fetching compressed mmCIF 7ei1 from http://files.rcsb.org/download/7ei1.cif 7ei1 title: Structure of Pyrococcus furiosus Cas1Cas2 complex [more info...] Chain information for 7ei1 #3 --- Chain | Description | UniProt A B C D E F G H I J K L M N O P | CRISPR-associated endonuclease Cas1 | I6TWX9_9EURY 1-322 Q R S T U V W X | CRISPR-associated endoribonuclease Cas2 | I6V1H0_9EURY 1-85 7ei1 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > sym #3 assembly 1 Made 1 copies for 7ei1 assembly 1 > view > ~tile > hide #!7 models > mmaker #4.1 to #1 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 4p6i, chain D (#1) with 7ei1, chain A (#4.1), sequence alignment score = 297.5 RMSD between 119 pruned atom pairs is 1.271 angstroms; (across all 266 pairs: 7.050) > mmaker #2 to #1 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 4p6i, chain F (#1) with apo-Refinement17-chains-corrected- renamed.cif, chain E (#2), sequence alignment score = 422.2 RMSD between 135 pruned atom pairs is 1.201 angstroms; (across all 266 pairs: 5.970) > hide #!2 models > select add #1 9925 atoms, 10115 bonds, 3 pseudobonds, 1291 residues, 2 models selected > show #!3 models > close #3 > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.99255,-0.015265,-0.12088,186.71,0.1034,0.4193,-0.90194,163.19,0.064453,-0.90772,-0.4146,268.65 > view matrix models > #1,-0.98859,-0.093934,-0.11774,192.31,0.071497,0.39536,-0.91574,166,0.13257,-0.91371,-0.38414,266.82 > ui mousemode right ""translate selected models"" > view matrix models > #1,-0.98859,-0.093934,-0.11774,188.56,0.071497,0.39536,-0.91574,175.47,0.13257,-0.91371,-0.38414,268.41 > mmaker #4 to #1 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 4p6i, chain D (#1) with 7ei1, chain A (#4.1), sequence alignment score = 297.5 RMSD between 119 pruned atom pairs is 1.271 angstroms; (across all 266 pairs: 7.050) > view matrix models > #1,-0.98859,-0.093934,-0.11774,261.89,0.071497,0.39536,-0.91574,158.38,0.13257,-0.91371,-0.38414,338.97 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.008205,0.96713,0.25413,152.5,0.39377,-0.23673,0.8882,160.99,0.91917,0.092782,-0.38277,246.06 > view matrix models > #1,0.22181,0.93253,0.28493,149.21,0.55141,-0.36096,0.7521,168.93,0.8042,-0.0097089,-0.59428,260.57 > view matrix models > #1,0.23316,0.9639,0.12855,149.73,0.53241,-0.23715,0.81259,159.14,0.81375,-0.12102,-0.56848,267.97 > ui mousemode right ""translate selected models"" > view matrix models > #1,0.23316,0.9639,0.12855,70.434,0.53241,-0.23715,0.81259,180.55,0.81375,-0.12102,-0.56848,206.48 > view matrix models > #1,0.23316,0.9639,0.12855,121.24,0.53241,-0.23715,0.81259,132.74,0.81375,-0.12102,-0.56848,92.59 > view matrix models > #1,0.23316,0.9639,0.12855,63.006,0.53241,-0.23715,0.81259,184.48,0.81375,-0.12102,-0.56848,205.37 > show #!5 models > show #!6 models > show sel cartoons > show sel atoms > show sel surfaces > select add #5 17017 atoms, 17386 bonds, 3 pseudobonds, 2179 residues, 9 models selected > select add #6 24109 atoms, 24657 bonds, 3 pseudobonds, 3067 residues, 11 models selected > select subtract #1 14184 atoms, 14542 bonds, 1776 residues, 10 models selected > color (#!5-6 & sel) #758ec4ff > hide sel surfaces > hide sel atoms > select subtract #5 7092 atoms, 7271 bonds, 888 residues, 3 models selected > select subtract #6 1 model selected > hide #!5 models > hide #!6 models > hide #!4 models > hide #!4.1 models > select #1/A 792 atoms, 807 bonds, 101 residues, 1 model selected > select #1/A-B 1547 atoms, 1576 bonds, 198 residues, 1 model selected > show sel atoms > show sel cartoons > show sel surfaces > color (#!1 & sel) #ce9bc2ff > select #1/D-F 6298 atoms, 6419 bonds, 3 pseudobonds, 823 residues, 2 models selected > select #1/D,F 4319 atoms, 4405 bonds, 2 pseudobonds, 564 residues, 2 models selected > color (#!1 & sel) #c0b59dff > select #1/C,E 4059 atoms, 4134 bonds, 1 pseudobond, 529 residues, 2 models selected > color (#!1 & sel) #98877cff > select add #1 9925 atoms, 10115 bonds, 3 pseudobonds, 1291 residues, 4 models selected > select subtract #1 6 models selected > show #!2 models > hide #!1 models > color #2/a:1-94/b:1-94 #d799c4 > color #2/a:95-end/b:95-end #6d8fc9 > color #2/f,e #c2b59bff > color #2/c,d #9c857a > show #!1 models > show #!4 models > hide #!2 models > hide #!1 models > hide #!4 models > show #!4 models > show #!4.1 models > select /4.1/R,Q Expected an objects specifier or a keyword > select #4.1/R,Q 2814 atoms, 2836 bonds, 168 residues, 1 model selected > color sel #ffffffff > color sel #ce9bc2ff > select #4.1/A,I 10039 atoms, 10146 bonds, 2 pseudobonds, 623 residues, 2 models selected > color (#!4.1 & sel) #c0b59dff > select #4.1/B,J 9865 atoms, 9969 bonds, 4 pseudobonds, 615 residues, 2 models selected > color (#!4.1 & sel) #98877cff > select add #4.1 22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 2 models selected > select add #4 22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 3 models selected > select subtract #4 Nothing selected > select add #4.1 22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 2 models selected > select add #4 22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 3 models selected > select subtract #4.1 1 model selected > select add #4 22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 3 models selected > select subtract #4 Nothing selected > show #!1 models > show #!2 models > hide #!2 models > mmaker #4/Q,R to #1/A,B 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 4p6i, chain A (#1) with 7ei1, chain Q (#4.1), sequence alignment score = 82.8 RMSD between 46 pruned atom pairs is 0.841 angstroms; (across all 78 pairs: 13.045) > hide #!1#!4.1 surfaces > tile 2 models tiled > ~tile tile > tile off tile Expected a models specifier or a keyword > ~tile > mmaker #4/Q,R to #1/A,B 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 4p6i, chain A (#1) with 7ei1, chain Q (#4.1), sequence alignment score = 82.8 RMSD between 46 pruned atom pairs is 0.841 angstroms; (across all 78 pairs: 13.045) > mmaker #2/A,B:1-100 to #1/A,B 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 4p6i, chain A (#1) with apo-Refinement17-chains-corrected- renamed.cif, chain A (#2), sequence alignment score = 63.8 RMSD between 41 pruned atom pairs is 1.076 angstroms; (across all 80 pairs: 7.338) > show #!2 models > hide #!1-2#!4.1 surfaces > hide #!1-2#!4.1 atoms > preset cartoons/nucleotides cylinders/stubs Using preset: Cartoons/Nucleotides / Cylinders/Stubs Changed 102371 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh tube rad 2 sides 24 thick 0.6 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides stubs > tile 3 models tiled > undo > lighting flat > lighting soft > lighting shadows true intensity 0.5 > lighting flat > lighting soft > tile 3 models tiled > undo > ui tool show ""Side View"" > ui tool show ""Show Sequence Viewer"" > ui tool show ""Modeller Comparative"" > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #7/E #7/F Alignment identifier is 1 > sequence chain #1/C #1/D #1/E #1/F #7/A #7/B #7/C #7/D Alignment identifier is 2 > sequence chain #2/A #2/B Alignment identifier is 3 > sequence chain #2/C #2/D #2/E #2/F Alignment identifier is 4 > sequence chain #4.1/A #4.1/B #4.1/I #4.1/J Alignment identifier is 5 > sequence chain #4.1/Q #4.1/R Alignment identifier is 6 > hide #!1 models > hide #!4 models > show #!1 models > show #!4 models > hide #!1 models > hide #!2 models > select #4/Q,R:16,18,19,22 169 atoms, 163 bonds, 8 residues, 1 model selected > show #!2 models > show #!1 models > select add #1 10094 atoms, 10278 bonds, 3 pseudobonds, 1299 residues, 3 models selected > select add #2 64299 atoms, 65093 bonds, 3 pseudobonds, 4747 residues, 10 models selected > select add #4 86848 atoms, 87881 bonds, 9 pseudobonds, 6145 residues, 18 models selected > show sel surfaces > hide sel cartoons > transparency (#!1-2#!4.1 & sel) 10 > transparency (#!1-2#!4.1 & sel) 90 > select subtract #1 76923 atoms, 77766 bonds, 6 pseudobonds, 4854 residues, 22 models selected > select subtract #2 22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 15 models selected > select subtract #4 6 models selected > hide #!2 models > hide #!1 models > select #4/Q,R:16,18,19,22 169 atoms, 163 bonds, 8 residues, 1 model selected > color (#!4.1 & sel) black > transparency (#!4.1 & sel) 0 > select #4/B,J:192,269,273 136 atoms, 130 bonds, 6 residues, 1 model selected > color (#!4.1 & sel) black > transparency (#!4.1 & sel) 0 > select #4/I,A:45,54,68,79 144 atoms, 142 bonds, 8 residues, 1 model selected > select #4/I,A:45,54 64 atoms, 64 bonds, 4 residues, 1 model selected > select #4/I,A:45,54,68,79 144 atoms, 142 bonds, 8 residues, 1 model selected > select #4/B,J:45,54,68,79 144 atoms, 142 bonds, 8 residues, 1 model selected > select #4/I,A:45,54,68,79 144 atoms, 142 bonds, 8 residues, 1 model selected > select #4/B,J,I,A:45,54,68,79 288 atoms, 284 bonds, 16 residues, 1 model selected > select add #4 22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 7 models selected > select subtract #4 6 models selected > show #!2 models > show #!1 models > hide #!2 models > hide #!4 models > select #1/A-B:77,16,78 #1/F,D:41,66 #1/E,C:59,248,245,163,84 220 atoms, 202 bonds, 20 residues, 1 model selected > color (#!1 & sel) black > transparency (#!1 & sel) 0 > select add #1 9925 atoms, 10115 bonds, 3 pseudobonds, 1291 residues, 8 models selected > select subtract #1 6 models selected > show #!4 models > hide #!1 models > select #4/B,J,I,A:45,54,68,79 288 atoms, 284 bonds, 16 residues, 1 model selected > select add #4 22718 atoms, 22951 bonds, 6 pseudobonds, 1406 residues, 7 models selected > select subtract #4 6 models selected > show #!1 models > hide #!4 models > show #!2 models > hide #!1 models > select #2/G:93,94,99, 91,95,92 #2/H:11,18 #2/A:67,27,32 62 atoms, 59 bonds, 3 residues, 1 model selected > select #2/A,B:93,94,99, 91,95,92 #2/A,B:11,18 #2/E,F:67,27,32 406 atoms, 392 bonds, 22 residues, 1 model selected > color (#!2 & sel) black > transparency (#!2 & sel) 0 > hide #!2 models > select add #2 54205 atoms, 54815 bonds, 3448 residues, 5 models selected > select subtract #2 6 models selected > show #!1 models > show #!2 models > show #!4 models > tile 3 models tiled > undo > hide #!2 models > hide #!4 models > show #!2 models > hide #!1 models > show #!4 models > hide #!4 models > select #2/D:1-7 98 atoms, 98 bonds, 7 residues, 1 model selected > hide sel surfaces > save /Users/whenriques/wiedenheft/projects/1-f-integration- > complex/paper.drafts/integration_paper_2/draft_20240525/main.figures/figure1/comparative.cas12.across.systems/chimera.pngs/IF- > pseudomonas.png width 864 height 670 supersample 3 transparentBackground > true > show #!1 models > hide #!2 models > save /Users/whenriques/wiedenheft/projects/1-f-integration- > complex/paper.drafts/integration_paper_2/draft_20240525/main.figures/figure1/comparative.cas12.across.systems/chimera.pngs/IE- > ecoli.png width 864 height 670 supersample 3 transparentBackground true > hide #!1 models > show #!4 models > save /Users/whenriques/wiedenheft/projects/1-f-integration- > complex/paper.drafts/integration_paper_2/draft_20240525/main.figures/figure1/comparative.cas12.across.systems/chimera.pngs/IA- > IG-IIIB-pfuriosis.png width 864 height 670 supersample 3 > transparentBackground true > show #!7 models > show #!6 models > hide #!6 models > hide #!7 models > show #!2 models > hide #!4 models > save /Users/whenriques/wiedenheft/projects/1-f-integration- > complex/paper.drafts/integration_paper_2/draft_20240525/main.figures/figure1/comparative.cas12.across.systems/chimera.pngs/dna- > binding-comparison.cxs includeMaps true > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-prespacer-bound/phenix/J1222-local- > refine/RealSpaceRefine_2/trimmed-8flj- > AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- > renamed_real_space_refined_002.pdb Chain information for trimmed-8flj- AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- renamed_real_space_refined_002.pdb #1 --- Chain | Description A | No description available B | No description available C | No description available E | No description available G | No description available H | No description available > color #2/g,h #f69320ff > color #1,2,3/a:1-94/b:1-94 #d799c4 > color #1,2,3/a:95-end/b:95-end #6d8fc9ff > color #1,2,3/f,e #c2b59bff > color #1,2,3/c,d #9c857a > color #1/g:1-27/h:1-27 #f69320ff > color #1/g:28-end/h:28-56 #92278f > color #1/i/h:57-end #939598 > color #1/m,k #d91b5d > color #1/l,j #a51e23 > color #1/g:1-27/h:1-27 #f69320ff > set bgColor white > lighting soft > select /C 4188 atoms, 4233 bonds, 303 residues, 1 model selected > show sel surfaces > select /G 854 atoms, 922 bonds, 27 residues, 1 model selected > style sel stick Changed 854 atom styles > select add #1 21746 atoms, 22179 bonds, 1844 residues, 1 model selected > select subtract #1 1 model selected > select /E 4942 atoms, 4994 bonds, 315 residues, 1 model selected > show sel surfaces > hbonds sel reveal true 261 hydrogen bonds found > hbonds sel reveal true 261 hydrogen bonds found > select add #1 21746 atoms, 22179 bonds, 261 pseudobonds, 1844 residues, 3 models selected > select subtract #1 2 models selected > select add #1 21746 atoms, 22179 bonds, 261 pseudobonds, 1844 residues, 2 models selected > select subtract #1 2 models selected > hbonds reveal true 1456 hydrogen bonds found > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /C LEU 149 /C GLU 150 /C ASP 151 /C ARG 152 /C VAL 153 /C LEU 154 /C ARG 155 /C ASP 156 /C PHE 159 /C VAL 161 /C ASP 162 /C THR 164 /C LEU 166 /C VAL 168 /C VAL 170 /C GLU 171 /C ASP 172 /C SER 173 /C ARG 175 /C LEU 177 /C GLU 178 /C GLN 179 /C ASN 182 /C HIS 183 /C GLU 184 /C HIS 185 /C LEU 186 /C LEU 187 /C THR 188 /C GLU 189 /C GLU 190 /C ARG 192 /C LEU 193 /C SER 194 /C LYS 195 /C ARG 196 /C LEU 197 /C PHE 198 /C LYS 199 /C LEU 200 /C GLN 203 /C THR 205 /C ARG 206 /C TYR 207 /C GLU 209 /C PHE 210 /C VAL 211 /C ARG 212 /C LYS 214 /C ARG 215 /C SER 217 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /A LYS 100 H bonded to atom that should not have hydrogens (/A LYS 100 C) > coulombic The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /C LEU 149 /C GLU 150 /C ASP 151 /C ARG 152 /C VAL 153 /C LEU 154 /C ARG 155 /C ASP 156 /C PHE 159 /C VAL 161 /C ASP 162 /C THR 164 /C LEU 166 /C VAL 168 /C VAL 170 /C GLU 171 /C ASP 172 /C SER 173 /C ARG 175 /C LEU 177 /C GLU 178 /C GLN 179 /C ASN 182 /C HIS 183 /C GLU 184 /C HIS 185 /C LEU 186 /C LEU 187 /C THR 188 /C GLU 189 /C GLU 190 /C ARG 192 /C LEU 193 /C SER 194 /C LYS 195 /C ARG 196 /C LEU 197 /C PHE 198 /C LYS 199 /C LEU 200 /C GLN 203 /C THR 205 /C ARG 206 /C TYR 207 /C GLU 209 /C PHE 210 /C VAL 211 /C ARG 212 /C LYS 214 /C ARG 215 /C SER 217 Using Amber 20 recommended default charges and atom types for standard residues Hydrogen /A LYS 100 H bonded to atom that should not have hydrogens (/A LYS 100 C) > select /C 4188 atoms, 4233 bonds, 208 pseudobonds, 303 residues, 2 models selected > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /C LEU 149 /C GLU 150 /C ASP 151 /C ARG 152 /C VAL 153 /C LEU 154 /C ARG 155 /C ASP 156 /C PHE 159 /C VAL 161 /C ASP 162 /C THR 164 /C LEU 166 /C VAL 168 /C VAL 170 /C GLU 171 /C ASP 172 /C SER 173 /C ARG 175 /C LEU 177 /C GLU 178 /C GLN 179 /C ASN 182 /C HIS 183 /C GLU 184 /C HIS 185 /C LEU 186 /C LEU 187 /C THR 188 /C GLU 189 /C GLU 190 /C ARG 192 /C LEU 193 /C SER 194 /C LYS 195 /C ARG 196 /C LEU 197 /C PHE 198 /C LYS 199 /C LEU 200 /C GLN 203 /C THR 205 /C ARG 206 /C TYR 207 /C GLU 209 /C PHE 210 /C VAL 211 /C ARG 212 /C LYS 214 /C ARG 215 /C SER 217 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIS (net charge -3) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmp18wu4sxi/ante.in.mol2 -fi mol2 -o /var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmp18wu4sxi/ante.out.mol2 -fo mol2 -c bcc -nc -3 -j 5 -s 2 -dr n (HIS) `` (HIS) `Welcome to antechamber 20.0: molecular input file processor.` (HIS) `` (HIS) `Info: Finished reading file (/var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmp18wu4sxi/ante.in.mol2); atoms read (19), bonds read (18).` (HIS) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIS) `` (HIS) `` (HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HIS) `Info: Total number of electrons: 78; net charge: -3` (HIS) `` (HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HIS) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HIS) `Cannot properly run ""/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".` Contents of sqm.out: -------------------------------------------------------- AMBER SQM VERSION 19 By Ross C. Walker, Michael F. Crowley, Scott Brozell, Tim Giese, Andreas W. Goetz, Tai-Sung Lee and David A. Case -------------------------------------------------------- -------------------------------------------------------------------------------- QM CALCULATION INFO -------------------------------------------------------------------------------- | QMMM: Citation for AMBER QMMM Run: | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008 QMMM: SINGLET STATE CALCULATION QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29 | QMMM: *** Selected Hamiltonian *** | QMMM: AM1 | QMMM: *** Parameter sets in use *** | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: *** SCF convergence criteria *** | QMMM: Energy change : 0.1D-07 kcal/mol | QMMM: Error matrix |FP-PF| : 0.1D+00 au | QMMM: Density matrix change : 0.5D-05 | QMMM: Maximum number of SCF cycles : 1000 | QMMM: *** Diagonalization Routine Information *** | QMMM: Pseudo diagonalizations are allowed. | QMMM: Auto diagonalization routine selection is in use. | QMMM: | QMMM: Timing diagonalization routines: | QMMM: norbs = 49 | QMMM: diag iterations used for timing = 20 | QMMM: | QMMM: Internal diag routine = 0.007674 seconds | QMMM: Dspev diag routine = 0.008439 seconds | QMMM: Dspevd diag routine = 0.007529 seconds | QMMM: Dspevx diag routine = 0.032484 seconds | QMMM: Dsyev diag routine = 0.009132 seconds | QMMM: Dsyevd diag routine = 0.008580 seconds | QMMM: Dsyevr diag routine = 0.009147 seconds | QMMM: | QMMM: Pseudo diag routine = 0.001625 seconds | QMMM: | QMMM: Using dspevd routine (diag_routine=3). QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1 N 245.8740 187.3160 181.6970 QMMM: 2 2 C 244.8840 188.2690 182.1990 QMMM: 3 3 C 244.1270 188.9350 181.0550 QMMM: 4 4 O 242.9040 189.1030 181.1230 QMMM: 5 5 C 245.5660 189.3220 183.0700 QMMM: 6 6 H 246.6860 187.4990 181.9310 QMMM: 7 7 H 244.2350 187.8100 182.7590 QMMM: 8 8 C 245.4960 186.2640 180.9570 QMMM: 9 9 C 246.6290 185.3770 180.4390 QMMM: 10 10 H 247.4480 186.0090 180.0650 QMMM: 11 11 H 247.0000 184.7420 181.2570 QMMM: 12 12 H 246.2540 184.7420 179.6230 QMMM: 13 13 N 244.8400 189.3330 179.9990 QMMM: 14 14 C 244.1830 189.9850 178.8700 QMMM: 15 15 H 244.2510 191.0770 178.9860 QMMM: 16 16 H 244.6780 189.6850 177.9350 QMMM: 17 17 H 243.1250 189.6850 178.8380 QMMM: 18 18 O 244.3130 186.0220 180.6900 QMMM: 19 19 H 245.6920 189.2380 179.9160 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- QMMM: ERROR! QMMM: Unable to achieve self consistency to the tolerances specified QMMM: No convergence in SCF after 1000 steps. QMMM: E = -0.2032E+06 DeltaE = -0.2880E-06 DeltaP = 0.1291E-04 QMMM: Smallest DeltaE = -0.2880E-06 DeltaP = 0.1291E-04 Step = 1000 Failure running ANTECHAMBER for residue HIS Check reply log for details > addh Summary of feedback from adding hydrogens to trimmed-8flj- AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- renamed_real_space_refined_002.pdb #1 --- warnings | Not adding hydrogens to /C LEU 149 CB because it is missing heavy- atom bond partners Not adding hydrogens to /C GLU 150 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C ASP 151 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C ARG 152 CB because it is missing heavy-atom bond partners Not adding hydrogens to /C VAL 153 CB because it is missing heavy-atom bond partners 48 messages similar to the above omitted notes | No usable SEQRES records for trimmed-8flj- AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- renamed_real_space_refined_002.pdb (#1) chain A; guessing termini instead No usable SEQRES records for trimmed-8flj- AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- renamed_real_space_refined_002.pdb (#1) chain B; guessing termini instead No usable SEQRES records for trimmed-8flj- AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- renamed_real_space_refined_002.pdb (#1) chain C; guessing termini instead No usable SEQRES records for trimmed-8flj- AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- renamed_real_space_refined_002.pdb (#1) chain E; guessing termini instead No usable SEQRES records for trimmed-8flj- AFCas3_real_space_refined_001-coot-0-cas23-joined-chains- renamed_real_space_refined_002.pdb (#1) chain G; guessing termini instead 1 messages similar to the above omitted Chain-initial residues that are actual N termini: /A MET 1, /B MET 1 Chain-initial residues that are not actual N termini: /C ASN 19, /E GLU 8 Chain-final residues that are actual C termini: /A ASN 1076 Chain-final residues that are not actual C termini: /B ARG 99, /C THR 321, /E VAL 322 1464 hydrogen bonds /B ARG 99 is not terminus, removing H atom from 'C' /C THR 321 is not terminus, removing H atom from 'C' /E VAL 322 is not terminus, removing H atom from 'C' 7607 hydrogens added > hbonds sel reveal true 224 hydrogen bonds found > coulombic sel The following residues are missing heavy (non-hydrogen) atoms, which may result in inaccurate electrostatics: /C LEU 149 /C GLU 150 /C ASP 151 /C ARG 152 /C VAL 153 /C LEU 154 /C ARG 155 /C ASP 156 /C PHE 159 /C VAL 161 /C ASP 162 /C THR 164 /C LEU 166 /C VAL 168 /C VAL 170 /C GLU 171 /C ASP 172 /C SER 173 /C ARG 175 /C LEU 177 /C GLU 178 /C GLN 179 /C ASN 182 /C HIS 183 /C GLU 184 /C HIS 185 /C LEU 186 /C LEU 187 /C THR 188 /C GLU 189 /C GLU 190 /C ARG 192 /C LEU 193 /C SER 194 /C LYS 195 /C ARG 196 /C LEU 197 /C PHE 198 /C LYS 199 /C LEU 200 /C GLN 203 /C THR 205 /C ARG 206 /C TYR 207 /C GLU 209 /C PHE 210 /C VAL 211 /C ARG 212 /C LYS 214 /C ARG 215 /C SER 217 Using Amber 20 recommended default charges and atom types for standard residues Assigning partial charges to residue HIS (net charge -3) with am1-bcc method Running ANTECHAMBER command: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber -ek qm_theory='AM1', -i /var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmphwt5bo5n/ante.in.mol2 -fi mol2 -o /var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmphwt5bo5n/ante.out.mol2 -fo mol2 -c bcc -nc -3 -j 5 -s 2 -dr n (HIS) `` (HIS) `Welcome to antechamber 20.0: molecular input file processor.` (HIS) `` (HIS) `Info: Finished reading file (/var/folders/4j/dgkkn5fn7p14vdghmyn16rzh0000gn/T/tmphwt5bo5n/ante.in.mol2); atoms read (19), bonds read (18).` (HIS) `Info: Determining atomic numbers from atomic symbols which are case sensitive.` (HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/bondtype -j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac` (HIS) `` (HIS) `` (HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff` (HIS) `Info: Total number of electrons: 78; net charge: -3` (HIS) `` (HIS) `Running: /Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out` (HIS) `/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/antechamber: Fatal Error!` (HIS) `Cannot properly run ""/Applications/ChimeraX-1.6.1.app/Contents/bin/amber20/bin/sqm -O -i sqm.in -o sqm.out"".` Contents of sqm.out: -------------------------------------------------------- AMBER SQM VERSION 19 By Ross C. Walker, Michael F. Crowley, Scott Brozell, Tim Giese, Andreas W. Goetz, Tai-Sung Lee and David A. Case -------------------------------------------------------- -------------------------------------------------------------------------------- QM CALCULATION INFO -------------------------------------------------------------------------------- | QMMM: Citation for AMBER QMMM Run: | QMMM: R.C. Walker, M.F. Crowley and D.A. Case, J. COMP. CHEM. 29:1019, 2008 QMMM: SINGLET STATE CALCULATION QMMM: RHF CALCULATION, NO. OF DOUBLY OCCUPIED LEVELS = 29 | QMMM: *** Selected Hamiltonian *** | QMMM: AM1 | QMMM: *** Parameter sets in use *** | QMMM: N : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: C : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: O : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: H : M.J.S.DEWAR et al. JACS, 107, 3902, (1985) | QMMM: *** SCF convergence criteria *** | QMMM: Energy change : 0.1D-07 kcal/mol | QMMM: Error matrix |FP-PF| : 0.1D+00 au | QMMM: Density matrix change : 0.5D-05 | QMMM: Maximum number of SCF cycles : 1000 | QMMM: *** Diagonalization Routine Information *** | QMMM: Pseudo diagonalizations are allowed. | QMMM: Auto diagonalization routine selection is in use. | QMMM: | QMMM: Timing diagonalization routines: | QMMM: norbs = 49 | QMMM: diag iterations used for timing = 20 | QMMM: | QMMM: Internal diag routine = 0.007498 seconds | QMMM: Dspev diag routine = 0.008459 seconds | QMMM: Dspevd diag routine = 0.007679 seconds | QMMM: Dspevx diag routine = 0.032344 seconds | QMMM: Dsyev diag routine = 0.009111 seconds | QMMM: Dsyevd diag routine = 0.008656 seconds | QMMM: Dsyevr diag routine = 0.012212 seconds | QMMM: | QMMM: Pseudo diag routine = 0.001643 seconds | QMMM: | QMMM: Using internal diagonalization routine (diag_routine=1). QMMM: QM Region Cartesian Coordinates (*=link atom) QMMM: QM_NO. MM_NO. ATOM X Y Z QMMM: 1 1 N 245.8740 187.3160 181.6970 QMMM: 2 2 C 244.8840 188.2690 182.1990 QMMM: 3 3 C 244.1270 188.9350 181.0550 QMMM: 4 4 O 242.9040 189.1030 181.1230 QMMM: 5 5 C 245.5660 189.3220 183.0700 QMMM: 6 6 H 246.6860 187.4990 181.9310 QMMM: 7 7 H 244.2350 187.8100 182.7590 QMMM: 8 8 C 245.4960 186.2640 180.9570 QMMM: 9 9 C 246.6290 185.3770 180.4390 QMMM: 10 10 H 247.4480 186.0090 180.0650 QMMM: 11 11 H 247.0000 184.7420 181.2570 QMMM: 12 12 H 246.2540 184.7420 179.6230 QMMM: 13 13 N 244.8400 189.3330 179.9990 QMMM: 14 14 C 244.1830 189.9850 178.8700 QMMM: 15 15 H 244.2510 191.0770 178.9860 QMMM: 16 16 H 244.6780 189.6850 177.9350 QMMM: 17 17 H 243.1250 189.6850 178.8380 QMMM: 18 18 H 245.6920 189.2380 179.9160 QMMM: 19 19 O 244.3130 186.0220 180.6900 -------------------------------------------------------------------------------- RESULTS -------------------------------------------------------------------------------- QMMM: ERROR! QMMM: Unable to achieve self consistency to the tolerances specified QMMM: No convergence in SCF after 1000 steps. QMMM: E = -0.2032E+06 DeltaE = -0.2880E-06 DeltaP = 0.1291E-04 QMMM: Smallest DeltaE = -0.2880E-06 DeltaP = 0.1291E-04 Step = 1000 Failure running ANTECHAMBER for residue HIS Check reply log for details > close session > open /Users/whenriques/Downloads/cryosparc_P28_J1806_006_volume_map.mrc Opened cryosparc_P28_J1806_006_volume_map.mrc as #1, grid size 336,336,336, pixel 1.07, shown at level 0.0536, step 2, values float32 > volume #1 step 1 > volume #1 level 0.1578 > volume #1 level 0.154 > volume #1 level 0.245 > volume #1 level 0.2222 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/cas123-apo-J411-C2.ccp4 Opened cas123-apo-J411-C2.ccp4 as #2, grid size 336,336,336, pixel 1.07, shown at level 0.039, step 2, values float32 > volume #2 step 1 > volume #2 level 0.238 > volume #1 level 0.1484 > volume flip #1 Opened cryosparc_P28_J1806_006_volume_map.mrc z flip as #3, grid size 336,336,336, pixel 1.07, shown at step 1, values float32 > ui mousemode right ""rotate selected models"" > select add #3 2 models selected > view matrix models > #3,0.38943,0.91875,-0.065088,-41.224,0.91129,-0.3946,-0.11767,103.87,-0.13379,-0.013489,-0.99092,380.57 > close #1 > fitmap #3 inMap #2 Fit map cryosparc_P28_J1806_006_volume_map.mrc z flip in map cas123-apo-J411-C2.ccp4 using 74318 points correlation = 0.9325, correlation about mean = 0.5093, overlap = 4056 steps = 88, shift = 4.77, angle = 8.01 degrees Position of cryosparc_P28_J1806_006_volume_map.mrc z flip (#3) relative to cas123-apo-J411-C2.ccp4 (#2) coordinates: Matrix rotation and translation 0.44950484 0.89327788 0.00016678 -60.69296899 0.89322366 -0.44947548 -0.01110331 101.93481576 -0.00984338 0.00513996 -0.99993834 357.99162458 Axis 0.85132024 0.52463871 -0.00284171 Axis point 0.00000000 68.66591985 179.17893225 Rotation angle (degrees) 179.45338739 Shift along axis 0.79248910 > select subtract #3 Nothing selected > volume #2 level 0.148 > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/RealSpaceRefine_17_chains_updated/apo- > Refinement17-chains-corrected-renamed.cif Summary of feedback from opening /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- complex/cryoem/cas1-2-3-apo/phenix/J411-alphafold/RealSpaceRefine_17_chains_updated/apo- Refinement17-chains-corrected-renamed.cif --- warnings | Atom H1 is not in the residue template for ARG /A:95 Atom H1 is not in the residue template for TYR /C:115 Atom H1 is not in the residue template for TYR /D:115 Atom H1 is not in the residue template for TYR /E:115 Atom H1 is not in the residue template for TYR /F:115 Chain information for apo-Refinement17-chains-corrected-renamed.cif #1 --- Chain | Description A B | No description available C D E F | No description available > fitmap #4 inMap #2 No atoms or maps for #4 > fitmap #1 inMap #2 Fit molecule apo-Refinement17-chains-corrected-renamed.cif (#1) to map cas123-apo-J411-C2.ccp4 (#2) using 54205 atoms average map value = 0.05567, steps = 380 shifted from previous position = 23.9 rotated from previous position = 28 degrees atoms outside contour = 46121, contour level = 0.148 Position of apo-Refinement17-chains-corrected-renamed.cif (#1) relative to cas123-apo-J411-C2.ccp4 (#2) coordinates: Matrix rotation and translation 0.94791798 0.10752863 -0.29981510 64.48967402 -0.20827382 0.92142338 -0.32802587 107.60805819 0.24098447 0.37338526 0.89582919 -102.33198106 Axis 0.74594025 -0.57513226 -0.33585119 Axis point 0.00000000 334.76833599 283.94750993 Rotation angle (degrees) 28.04418676 Shift along axis 20.58489514 > select add #1 54205 atoms, 54815 bonds, 3448 residues, 1 model selected > view matrix models > #1,0.24362,0.78341,0.57177,-106.17,-0.11127,0.60822,-0.78593,234.93,-0.96347,0.12785,0.23535,266.8 > fitmap #1 inMap #2 Fit molecule apo-Refinement17-chains-corrected-renamed.cif (#1) to map cas123-apo-J411-C2.ccp4 (#2) using 54205 atoms average map value = 0.1719, steps = 92 shifted from previous position = 8.52 rotated from previous position = 9.85 degrees atoms outside contour = 25406, contour level = 0.148 Position of apo-Refinement17-chains-corrected-renamed.cif (#1) relative to cas123-apo-J411-C2.ccp4 (#2) coordinates: Matrix rotation and translation 0.11504553 0.80202823 0.58610174 -96.24150302 -0.00313957 0.59030997 -0.80717055 230.66035293 -0.99335526 0.09102125 0.07043055 313.15822399 Axis 0.45194489 0.79473842 -0.40513783 Axis point 65.28499623 0.00000000 272.76301302 Rotation angle (degrees) 96.43678798 Shift along axis 12.94654506 > color #2/g,h #f69320ff > color #1,2,3/a:1-94/b:1-94 #d799c4 > color #1,2,3/a:95-end/b:95-end #6d8fc9ff > color #1,2,3/f,e #c2b59bff > color #1,2,3/c,d #9c857a > hide sel atoms > show sel cartoons > hide #!2 models > show #!2 models > hide #!3 models > set bgColor white > lighting soft > ui tool show ""Color Zone"" > color zone #2 near #1 distance 3 > show #!3 models > hide #!3 models > show #!3 models > volume #3 level 0.1208 > transparency 50 > hide #!2 models > volume #3 level 0.1484 > open /Users/whenriques/Downloads/cryosparc_P28_J1670_012_volume_map(1).mrc Opened cryosparc_P28_J1670_012_volume_map(1).mrc as #4, grid size 336,336,336, pixel 1.07, shown at level 0.0468, step 2, values float32 > volume #4 step 1 > volume #4 level 0.2464 > volume flip #4 Opened cryosparc_P28_J1670_012_volume_map(1).mrc z flip as #5, grid size 336,336,336, pixel 1.07, shown at step 1, values float32 > fitmap #5 inMap #2 Fit map cryosparc_P28_J1670_012_volume_map(1).mrc z flip in map cas123-apo-J411-C2.ccp4 using 19800 points correlation = 0.4882, correlation about mean = 0.05939, overlap = 476.6 steps = 288, shift = 10.6, angle = 16 degrees Position of cryosparc_P28_J1670_012_volume_map(1).mrc z flip (#5) relative to cas123-apo-J411-C2.ccp4 (#2) coordinates: Matrix rotation and translation 0.97763276 -0.11940625 -0.17313676 50.73415836 0.08606282 0.97825520 -0.18870601 24.55697789 0.19190461 0.16958454 0.96665077 -52.71673311 Axis 0.64999410 -0.66224111 0.37275245 Axis point 314.77138663 0.00000000 263.38712117 Rotation angle (degrees) 15.99840650 Shift along axis -2.93602838 > select subtract #1 Nothing selected > select add #5 2 models selected > view matrix models > #5,-0.97547,-0.035221,0.21731,361.41,-0.12706,0.89618,-0.42511,120.84,-0.17978,-0.44229,-0.87867,435.61 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.97547,-0.035221,0.21731,316.37,-0.12706,0.89618,-0.42511,142,-0.17978,-0.44229,-0.87867,450.85 > fitmap #5 inMap #2 Fit map cryosparc_P28_J1670_012_volume_map(1).mrc z flip in map cas123-apo-J411-C2.ccp4 using 19800 points correlation = 0.5822, correlation about mean = 0.04315, overlap = 606.2 steps = 124, shift = 10.2, angle = 11 degrees Position of cryosparc_P28_J1670_012_volume_map(1).mrc z flip (#5) relative to cas123-apo-J411-C2.ccp4 (#2) coordinates: Matrix rotation and translation -0.98080755 -0.07152921 0.18138394 332.08283830 -0.11658827 0.96079882 -0.25154088 89.10053568 -0.15628095 -0.26786043 -0.95069820 428.46616278 Axis -0.04785110 0.99007818 -0.13211913 Axis point 186.86976559 0.00000000 205.74097384 Rotation angle (degrees) 170.18169229 Shift along axis 15.71739182 > view matrix models > #5,-0.98081,-0.071529,0.18138,333.17,-0.11659,0.9608,-0.25154,90.553,-0.15628,-0.26786,-0.9507,427.8 > view matrix models > #5,-0.98081,-0.071529,0.18138,314.53,-0.11659,0.9608,-0.25154,104.4,-0.15628,-0.26786,-0.9507,429.49 > fitmap #5 inMap #2 Fit map cryosparc_P28_J1670_012_volume_map(1).mrc z flip in map cas123-apo-J411-C2.ccp4 using 19800 points correlation = 0.6087, correlation about mean = 0.0787, overlap = 672.3 steps = 216, shift = 20.9, angle = 34.5 degrees Position of cryosparc_P28_J1670_012_volume_map(1).mrc z flip (#5) relative to cas123-apo-J411-C2.ccp4 (#2) coordinates: Matrix rotation and translation -0.99809986 0.05125922 -0.03419326 353.47728620 0.03982020 0.96007352 0.27689927 -28.40170049 0.04702169 0.27501153 -0.96029039 295.10923181 Axis -0.02301041 -0.98996381 -0.13943517 Axis point 174.04105738 0.00000000 153.21286536 Rotation angle (degrees) 177.64911614 Shift along axis -21.16560966 > view matrix models > #5,-0.9981,0.051259,-0.034193,341.68,0.03982,0.96007,0.2769,-32.046,0.047022,0.27501,-0.96029,295.85 > ui mousemode right ""rotate selected models"" > view matrix models > #5,-0.97719,0.14004,-0.15966,344.72,0.15087,0.98686,-0.057804,-1.2959,0.14947,-0.080574,-0.98548,336.68 > view matrix models > #5,-0.9829,0.17567,-0.05526,322.29,0.18065,0.97802,-0.10416,2.0929,0.035748,-0.11236,-0.99302,365.84 > view matrix models > #5,-0.97844,0.18555,-0.090697,325.87,0.19494,0.97477,-0.10873,0.53705,0.068233,-0.12407,-0.98993,360.68 > view matrix models > #5,-0.88539,0.46296,-0.041951,254.42,0.45049,0.87679,0.16824,-82.307,0.11467,0.13006,-0.98485,309.76 > view matrix models > #5,-0.89253,0.44504,-0.072982,264.03,0.42445,0.88364,0.19756,-83.21,0.15241,0.14535,-0.97757,298.51 > view matrix models > #5,-0.89253,0.44504,-0.072982,266.36,0.42445,0.88364,0.19756,-87.173,0.15241,0.14535,-0.97757,301.07 > fitmap #5 inMap #2 Fit map cryosparc_P28_J1670_012_volume_map(1).mrc z flip in map cas123-apo-J411-C2.ccp4 using 19800 points correlation = 0.9412, correlation about mean = 0.4323, overlap = 1974 steps = 140, shift = 7.19, angle = 13.1 degrees Position of cryosparc_P28_J1670_012_volume_map(1).mrc z flip (#5) relative to cas123-apo-J411-C2.ccp4 (#2) coordinates: Matrix rotation and translation -0.86110360 0.50840669 0.00482061 242.48923124 0.50840603 0.86111626 -0.00145346 -66.17175483 -0.00489005 0.00119925 -0.99998733 357.65546782 Axis 0.26351887 0.96465424 -0.00006565 Axis point 130.74936482 0.00000000 178.50918917 Rotation angle (degrees) 179.71161577 Shift along axis 0.04414403 > volume #4 level 0.217 > volume #5 level 0.1352 > view matrix models > #5,-0.099665,0.74318,0.66163,-54.49,0.73613,0.50245,-0.45349,27.331,-0.66946,0.44185,-0.59715,342.42 > undo > volume #5 level 0.2006 > hide #!3 models > volume #5 level 0.1384 > volume #5 level 0.1123 > volume #5 level 0.1286 > transparency sel 50 > select subtract #5 Nothing selected > volume #5 level 0.2104 > open /Users/whenriques/Downloads/cryosparc_P17_J760_002_volume_map.mrc Opened cryosparc_P17_J760_002_volume_map.mrc as #6, grid size 200,200,200, pixel 2.3, shown at level 0.0742, step 1, values float32 > open /Users/whenriques/Downloads/cryosparc_P17_J759_002_volume_map.mrc Opened cryosparc_P17_J759_002_volume_map.mrc as #7, grid size 200,200,200, pixel 2.3, shown at level 0.0756, step 1, values float32 > open /Users/whenriques/Downloads/cryosparc_P17_J758_002_volume_map.mrc Opened cryosparc_P17_J758_002_volume_map.mrc as #8, grid size 200,200,200, pixel 2.3, shown at level 0.0551, step 1, values float32 > undo > close #1 > close #2 > close #3-5 > volume #8 level 0.1751 > volume #8 level 0.09729 > volume flip * Missing or invalid ""volumes"" argument: invalid density maps specifier > volume flip #6-8 Opened cryosparc_P17_J760_002_volume_map.mrc z flip as #1, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 Opened cryosparc_P17_J759_002_volume_map.mrc z flip as #2, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 Opened cryosparc_P17_J758_002_volume_map.mrc z flip as #3, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 > tile 3 models tiled > volume #8 level 0.1881 > volume #8 level 0.2399 > undo > show #!6 models > hide #!8 models > hide #!6 models > close #6-8 > volume #3 level 0.214 > volume #1 level 0.2878 > volume #2 level 0.138 > volume #1 level 0.33 > volume #2 level 0.3 > volume #3 level 0.3 > volume #3 level 0.1087 > volume #3 level 0.3389 > lighting soft > volume #2 level 0.2844 > close session > open /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J764_002_volume_map.mrc > /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J763_003_volume_map.mrc > /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J762_002_volume_map.mrc > /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J761_002_volume_map.mrc > /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J760_002_volume_map.mrc > /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J759_002_volume_map.mrc > /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/cryosparc_P17_J758_002_volume_map.mrc Opened cryosparc_P17_J764_002_volume_map.mrc as #1.1, grid size 200,200,200, pixel 2.3, shown at level 0.044, step 1, values float32 Opened cryosparc_P17_J763_003_volume_map.mrc as #1.2, grid size 200,200,200, pixel 2.3, shown at level 0.0354, step 1, values float32 Opened cryosparc_P17_J762_002_volume_map.mrc as #1.3, grid size 200,200,200, pixel 2.3, shown at level 0.0364, step 1, values float32 Opened cryosparc_P17_J761_002_volume_map.mrc as #1.4, grid size 200,200,200, pixel 2.3, shown at level 0.0479, step 1, values float32 Opened cryosparc_P17_J760_002_volume_map.mrc as #1.5, grid size 200,200,200, pixel 2.3, shown at level 0.0742, step 1, values float32 Opened cryosparc_P17_J759_002_volume_map.mrc as #1.6, grid size 200,200,200, pixel 2.3, shown at level 0.0756, step 1, values float32 Opened cryosparc_P17_J758_002_volume_map.mrc as #1.7, grid size 200,200,200, pixel 2.3, shown at level 0.0551, step 1, values float32 > volume flip #1 Opened cryosparc_P17_J764_002_volume_map.mrc z flip as #2, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 Opened cryosparc_P17_J763_003_volume_map.mrc z flip as #3, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 Opened cryosparc_P17_J762_002_volume_map.mrc z flip as #4, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 Opened cryosparc_P17_J761_002_volume_map.mrc z flip as #5, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 Opened cryosparc_P17_J760_002_volume_map.mrc z flip as #6, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 Opened cryosparc_P17_J759_002_volume_map.mrc z flip as #7, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 Opened cryosparc_P17_J758_002_volume_map.mrc z flip as #8, grid size 200,200,200, pixel 2.3, shown at step 1, values float32 > close #1#1.1-7 > set bgColor white > lighting soft > volume #2 level 0.3 > volume #4 level 0.3 > volume #3 level 0.3 > volume #5 level 0.3 > volume #6 level 0.3 > volume #7 level 0.3 > volume #8 level 0.3 > tile 7 models tiled > volume #6 level 0.2 > volume #7 level 0.2 > volume #8 level 0.2 > volume #5 level 0.2 > volume #4 level 0.2 > volume #3 level 0.2 > volume #2 level 0.2 > volume #7 level 0.3404 > vop level 0.1 > vop level 0.3 > save /Users/whenriques/Dropbox/wiedenheft/projects/1-f-integration- > complex/cryoem/integration_complex/spermidine.Mn.data.collection.2022.10/pam_prespacer/cryosparc/P17/J758-J764-NURefines/volumes_flipped.cxs > includeMaps true ===== 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 - 86 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: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MJ123LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 13 days, 22 hours, 54 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: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal BenQ GW2760HS: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz 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-Clipper: 0.21.0 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.6.1 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.1 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.1 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.6.0 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-Label: 1.1.7 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.0.12 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.3.7 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.0 ChimeraX-NRRD: 1.0 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.10.1 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.8.3 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.10.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.1 ChimeraX-Topography: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.28.4 ChimeraX-uniprot: 2.2.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.0.7 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.39.3 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.8.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.35 imagecodecs: 2022.2.22 imagesize: 1.4.1 importlib-metadata: 6.6.0 ipykernel: 6.21.1 ipython: 8.10.0 ipython-genutils: 0.2.0 ipywidgets: 8.0.6 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.0.2 jupyter-core: 5.3.0 jupyterlab-widgets: 3.0.7 kiwisolver: 1.4.4 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.2 matplotlib: 3.6.3 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.6 netCDF4: 1.6.2 networkx: 2.8.8 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.23.5 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 9.3.0 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 can't reproduce all ChimeraX