id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17172 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 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 0x00007ff8481e7b00 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, lxml._elementpath, lxml.etree, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, chimerax.pdb_lib._load_libs, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, psutil._psutil_osx, psutil._psutil_posix, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, PIL._webp, chimerax.atom_search.ast, chimerax.chem_group._chem_group, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 65) {""app_name"":""ChimeraX"",""timestamp"":""2025-03-24 09:42:01.00 +0100"",""app_version"":""1.8.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""A085D66B-232F-4CF6-9DDA-1889DCAAB909""} { ""uptime"" : 240000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro16,1"", ""coalitionID"" : 1003, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-03-24 09:41:52.6629 +0100"", ""codeSigningMonitor"" : 0, ""incident"" : ""A085D66B-232F-4CF6-9DDA-1889DCAAB909"", ""pid"" : 9415, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-03-23 11:35:14.0950 +0100"", ""procStartAbsTime"" : 194046510541388, ""procExitAbsTime"" : 241616368391841, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.8.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.8.0"",""CFBundleVersion"":""1.8.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""C4027B15-248B-5659-BACC-6FB29543A4B7"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""8D528D7E-5C72-169F-357F-E09EC31F9564"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""bootSessionUUID"" : ""ECAC3F3E-CD7E-4414-A068-42C10232CC05"", ""wakeTime"" : 14, ""bridgeVersion"" : {""build"":""22P3060"",""train"":""9.3""}, ""sleepWakeUUID"" : ""BAD323D9-2941-45B6-94F8-A43071712230"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0 is not in any region. 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""factorPackIds"" : { }, ""deploymentId"" : 240000013 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open 1imp Summary of feedback from opening 1imp fetched from pdb --- note | Fetching compressed mmCIF 1imp from http://files.rcsb.org/download/1imp.cif 1imp title: Colicin E9 immunity protein IM9, NMR, 21 structures [more info...] Chain information for 1imp --- Chain | Description | UniProt 1.1/A 1.2/A 1.3/A 1.4/A 1.5/A 1.6/A 1.7/A 1.8/A 1.9/A 1.10/A 1.11/A 1.12/A 1.13/A 1.14/A 1.15/A 1.16/A 1.17/A 1.18/A 1.19/A 1.20/A 1.21/A | IM9 | IMM9_ECOLI 1-86 > hide #1.1 models > show #1.1 models > hide models > show #1.1 models > open 1fsj Summary of feedback from opening 1fsj fetched from pdb --- note | Fetching compressed mmCIF 1fsj from http://files.rcsb.org/download/1fsj.cif 1fsj title: Crystal structure of the E9 DNAse domain [more info...] Chain information for 1fsj #2 --- Chain | Description | UniProt B C D E | COLICIN E9 | CEA9_ECOLI 2-134 202-334 402-434 602-734 Non-standard residues in 1fsj #2 --- PO4 — phosphate ion ZN — zinc ion 1fsj mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly 4| author_defined_assembly > hide #!1 models Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds > hide #2 cartoons > show sel cartoons Drag select of 60 atoms, 4 pseudobonds, 55 bonds > hide sel atoms Drag select of 141 atoms, 8 pseudobonds, 127 bonds > hide sel atoms > select clear > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined2.pdb"" Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #3 --- Chain | Description Aa | No description available Ba | No description available Ca | No description available DA | No description available Da | No description available Db | No description available Dc | No description available Dd | No description available De | No description available Df | No description available EA | No description available FA | No description available > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_map_2p4Å.mrc"" Opened halfcleaved_HNH_center_main_map_2p4Å.mrc as #4, grid size 420,420,420, pixel 0.725, shown at level 0.0319, step 2, values float32 > volume #4 level 0.07 > volume #4 step 1 > hide #!4 models > style stick Changed 56061 atom styles > color #3/DA light gray > color #3/EA dim gray > color #3/FA dark red > color #3/Ca rebecca purple > color #3/Ba forest green > color #3/Da,Db,Dc,Dd,De,Df khaki > color #3/Aa steel blue > color #3/Aa:232-350 dark turquoise > hide #3 atoms > show #3 cartoons Drag select of 49 atoms, 132 residues, 4 pseudobonds, 43 bonds > ui mousemode right ""rotate selected models"" > view matrix models #2,1,0,0,82.662,0,1,0,181.25,0,0,1,114.9 > view matrix models > #2,1,0.0013443,-0.0025868,85.9,-0.0013444,1,-6.0428e-05,181.66,0.0025868,6.3905e-05,1,96.743 > mmaker sel to #3/Aa:230-350 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 halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with 1fsj, chain E (#2), sequence alignment score = 97 RMSD between 11 pruned atom pairs is 1.284 angstroms; (across all 97 pairs: 16.295) > color #2 yellow > color #2 byhetero > hide #!3 models > select subtract #2/E:700 1046 atoms, 43 bonds, 4 pseudobonds, 135 residues, 2 models selected > select subtract #2/E:701 1038 atoms, 39 bonds, 4 pseudobonds, 134 residues, 2 models selected > select subtract #2/E:702 1028 atoms, 32 bonds, 3 pseudobonds, 133 residues, 2 models selected > select subtract #2/E:703 1018 atoms, 25 bonds, 3 pseudobonds, 132 residues, 2 models selected > select subtract #2/E:719 1010 atoms, 25 bonds, 3 pseudobonds, 131 residues, 2 models selected > select subtract #2/E:720 999 atoms, 25 bonds, 3 pseudobonds, 130 residues, 2 models selected > select subtract #2/E:721 992 atoms, 25 bonds, 3 pseudobonds, 129 residues, 2 models selected > select subtract #2/E:722 985 atoms, 25 bonds, 3 pseudobonds, 128 residues, 2 models selected > select clear > select add #2/E:700 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/E:701 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #2/E:702 27 atoms, 25 bonds, 3 residues, 1 model selected > select add #2/E:703 37 atoms, 35 bonds, 4 residues, 1 model selected > select add #2/E:719 45 atoms, 43 bonds, 5 residues, 1 model selected > select add #2/E:720 56 atoms, 53 bonds, 6 residues, 1 model selected > select add #2/E:721 63 atoms, 59 bonds, 7 residues, 1 model selected > select add #2/E:722 70 atoms, 65 bonds, 8 residues, 1 model selected > hide #!2 models > show #!3 models > mmaker sel to #3/Aa:300-325 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 halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with 1fsj, chain E (#2), sequence alignment score = 33.3 RMSD between 6 pruned atom pairs is 0.986 angstroms; (across all 8 pairs: 2.082) > show #!2 models > view matrix models > #2,0.97297,-0.22873,-0.031935,103.66,0.22967,0.94372,0.23802,167.46,-0.024305,-0.23892,0.97073,110.17 > view matrix models > #2,0.97551,-0.19874,-0.094297,106.33,0.21196,0.96388,0.16128,171.49,0.058839,-0.17731,0.98239,106.64 > view matrix models > #2,0.97749,-0.14562,0.15266,94.724,0.17631,0.96123,-0.21202,189.82,-0.11586,0.23416,0.96527,111.65 > select clear > select #2/E:702 10 atoms, 10 bonds, 1 residue, 1 model selected > view matrix models > #2,0.98567,-0.047376,0.16189,94.269,0.055707,0.99733,-0.047316,185.39,-0.15921,0.055656,0.98567,112.54 > select #2/E:700 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/E:701 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #2/E:702 27 atoms, 25 bonds, 3 residues, 1 model selected > select add #2/E:703 37 atoms, 35 bonds, 4 residues, 1 model selected > select add #2/E:704 45 atoms, 42 bonds, 5 residues, 1 model selected > select add #2/E:706 52 atoms, 49 bonds, 6 residues, 1 model selected > select add #2/E:707 60 atoms, 56 bonds, 7 residues, 1 model selected > select add #2/E:708 66 atoms, 61 bonds, 8 residues, 1 model selected > select add #2/E:709 75 atoms, 69 bonds, 9 residues, 1 model selected > select add #2/E:710 79 atoms, 72 bonds, 10 residues, 1 model selected > mmaker sel to #3/Aa:300-314 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 halfcleaved_HNH_center_main_model_refined2.pdb, chain Aa (#3) with 1fsj, chain E (#2), sequence alignment score = 46.3 RMSD between 10 pruned atom pairs is 0.499 angstroms; (across all 10 pairs: 0.499) > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > select #3/Aa:280 11 atoms, 10 bonds, 1 residue, 1 model selected > show #3/Aa:305,280,328,304 > select #3/Aa:332 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > transparency 50 > hide #!4 models > hide #!3 models > hide #!2 models > select clear > show #!3 models > show #!2 models > combine #2 > hide #!2 models > hide #!3 models > show #5 cartoons > select #5/C:273 7 atoms, 7 bonds, 1 residue, 1 model selected > select up 72 atoms, 72 bonds, 10 residues, 1 model selected > select up 1047 atoms, 1071 bonds, 132 residues, 1 model selected > delete sel > select #5/D:407 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5/B:6 17 atoms, 15 bonds, 2 residues, 1 model selected > select up 86 atoms, 84 bonds, 10 residues, 1 model selected > select up 2111 atoms, 2159 bonds, 266 residues, 1 model selected > delete sel > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Structure/1fsj_E9_nuclease_HNH_like.pdb"" models #5 > select #5/E:904@ZN 1 atom, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > select up 6 atoms, 4 bonds, 2 residues, 1 model selected > select #5 1388 atoms, 1087 bonds, 7 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@P 1387 atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@O2 1386 atoms, 1083 bonds, 7 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@O3 1385 atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@O1 1384 atoms, 1083 bonds, 6 pseudobonds, 457 residues, 2 models selected > select subtract #5/E:804@O4 1383 atoms, 1083 bonds, 6 pseudobonds, 456 residues, 2 models selected > select subtract #5/E:904@ZN 1382 atoms, 1083 bonds, 3 pseudobonds, 455 residues, 2 models selected > delete sel > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Structure/zn_phosphate_from_1fsj.pdb"" models #5 > hide #!5 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!2 models > hide #!2 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/IFhnh_Manuscript/maps_and_models/NTS_cleaved/halfcleaved_HNH_center_main_model_refined_with_water.pdb"" Chain information for halfcleaved_HNH_center_main_model_refined_with_water.pdb #6 --- Chain | Description Aa | No description available Ba | No description available Ca | No description available DA | No description available Da | No description available Db | No description available Dc | No description available Dd | No description available De | No description available Df | No description available EA | No description available FA | No description available > style stick Changed 80248 atom styles > hide #6 atoms > show #6 cartoons > show #6/B atoms > show #6/D atoms > show #6/C atoms > show #6/A atoms > color #6/DA light gray > color #6/EA dim gray > color #6/FA dark red > color #6/Ca rebecca purple > color #6/Ba forest green > color #6/Da,Db,Dc,Dd,De,Df khaki > color #6/Aa steel blue > color #6/Aa:232-350 dark turquoise > color #6 byhetero > show #6/Aa:305,280,328 > show #6/Aa:304,280,328 > show #!5 models > hide #!5 models > show #!2 models > select #6/Aa:303 7 atoms, 6 bonds, 1 residue, 1 model selected > show #!3 models > hide #!3 models > show #!4 models > volume #4 level 0.09 > hide #!2 models > show #!2 models > hide #!4 models > select #6/Aa:332 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > lighting soft > lighting simple > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > select #6/Aa:302 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #2/E:700 18 atoms, 16 bonds, 2 residues, 2 models selected > show sel atoms > select #2/E:723 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #6/Aa:324 13 atoms, 11 bonds, 2 residues, 2 models selected > show sel atoms > open 1v14 Summary of feedback from opening 1v14 fetched from pdb --- note | Fetching compressed mmCIF 1v14 from http://files.rcsb.org/download/1v14.cif 1v14 title: Crystal Structure of the Colicin E9, mutant His103Ala, in complex with Mg+2 and dsDNA (resolution 2.9A) [more info...] Chain information for 1v14 #7 --- Chain | Description | UniProt A B C D | COLICIN E9 | CEA9_ECOLI 2-134 E F G H I J K L | 5'-D(*GP*CP*GP*AP*TP*CP*GP*CP)-3' | Non-standard residues in 1v14 #7 --- MG — magnesium ion 1v14 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 3| author_and_software_defined_assembly 4| author_and_software_defined_assembly > hide #!2 models > hide #!6 models > view > select add #7 5341 atoms, 5524 bonds, 73 pseudobonds, 623 residues, 5 models selected > select clear > select add #7 5328 atoms, 5513 bonds, 73 pseudobonds, 621 residues, 3 models selected > hide sel atoms > show sel cartoons > select clear > select add #7/G:8 19 atoms, 20 bonds, 1 residue, 1 model selected > select add #7/H:12 40 atoms, 43 bonds, 2 residues, 1 model selected > select add #7/J:11 62 atoms, 67 bonds, 3 residues, 1 model selected > select add #7/I:8 81 atoms, 87 bonds, 4 residues, 1 model selected > select add #7/C:80 87 atoms, 92 bonds, 5 residues, 1 model selected > select add #7/B:123 94 atoms, 98 bonds, 6 residues, 1 model selected > select add #7/E:5 114 atoms, 119 bonds, 7 residues, 1 model selected > select add #7/F:12 135 atoms, 142 bonds, 8 residues, 1 model selected > select add #7/A:53 146 atoms, 153 bonds, 9 residues, 1 model selected > select up 1143 atoms, 1247 bonds, 77 residues, 1 model selected > select up 3979 atoms, 4147 bonds, 438 residues, 1 model selected > hide sel cartoons > select clear > select #7/D:100 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #7/D:101 17 atoms, 15 bonds, 2 residues, 1 model selected > select add #7/D:102 27 atoms, 25 bonds, 3 residues, 1 model selected > select add #7/D:103 32 atoms, 29 bonds, 4 residues, 1 model selected > select add #7/D:104 40 atoms, 36 bonds, 5 residues, 1 model selected > select add #7/D:105 49 atoms, 44 bonds, 6 residues, 1 model selected > select add #7/D:106 56 atoms, 51 bonds, 7 residues, 1 model selected > select add #7/D:107 64 atoms, 58 bonds, 8 residues, 1 model selected > show #!6 models > mmaker sel to #6/Aa:300-310 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 halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa (#6) with 1v14, chain D (#7), sequence alignment score = 23.8 RMSD between 8 pruned atom pairs is 0.406 angstroms; (across all 8 pairs: 0.406) > color #7 yellow > color #7 byhetero > select clear > select #7/K:6 19 atoms, 20 bonds, 1 residue, 1 model selected > show #!4 models > hide #!4 models > show #!4 models > show sel atoms > select #7/K:5 20 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > view sel > select #7/D:5 11 atoms, 10 bonds, 1 residue, 1 model selected > hide #!4 models > select #7/D:102 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/D:6 18 atoms, 17 bonds, 2 residues, 1 model selected > select subtract #7/D:6 10 atoms, 10 bonds, 1 residue, 1 model selected > select add #7/D:5 21 atoms, 20 bonds, 2 residues, 1 model selected > select add #7/D:103 26 atoms, 24 bonds, 3 residues, 1 model selected > select add #7/D:100 35 atoms, 32 bonds, 4 residues, 1 model selected > select add #7/D:127 45 atoms, 42 bonds, 5 residues, 1 model selected > show sel atoms > style stick Changed 85576 atom styles > select add #7/K:4 66 atoms, 65 bonds, 6 residues, 1 model selected > select #7/K:5 20 atoms, 21 bonds, 1 residue, 1 model selected > select add #7/K:6 39 atoms, 41 bonds, 2 residues, 1 model selected > hide sel cartoons > select clear > show #!4 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb"" models #7 > hide #!4 models > hide #!6 models > hide #!7 models > show #!7 models > show #7 cartoons > view > select #7/H:12 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #7/G:8 40 atoms, 43 bonds, 2 residues, 1 model selected > select add #7/F:13 60 atoms, 64 bonds, 3 residues, 1 model selected > select add #7/E:7 82 atoms, 88 bonds, 4 residues, 1 model selected > select add #7/A:102 92 atoms, 98 bonds, 5 residues, 1 model selected > select add #7/J:12 113 atoms, 121 bonds, 6 residues, 1 model selected > select add #7/I:7 135 atoms, 145 bonds, 7 residues, 1 model selected > select add #7/C:78 141 atoms, 150 bonds, 8 residues, 1 model selected > select up 956 atoms, 1055 bonds, 56 residues, 1 model selected > select up 2934 atoms, 3079 bonds, 306 residues, 1 model selected > select up 2956 atoms, 3079 bonds, 328 residues, 1 model selected > select up 5328 atoms, 5513 bonds, 621 residues, 1 model selected > select down 2956 atoms, 3079 bonds, 328 residues, 1 model selected > delete sel > select #7/B:89 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 42 atoms, 42 bonds, 5 residues, 1 model selected > select up 1045 atoms, 1068 bonds, 132 residues, 1 model selected > delete sel > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Structure/1v14_E9_nuclease_his103_mut_with_dsDNA.pdb"" models #7 > hide #!7 models > open 1emv Summary of feedback from opening 1emv fetched from pdb --- note | Fetching compressed mmCIF 1emv from http://files.rcsb.org/download/1emv.cif 1emv title: Crystal structure of colicin E9 DNAse domain with its cognate immunity protein IM9 (1.7 angstroms) [more info...] Chain information for 1emv #8 --- Chain | Description | UniProt A | IMMUNITY PROTEIN IM9 | IMM9_ECOLI 1-86 B | COLICIN E9 | CEA9_ECOLI 2-134 Non-standard residues in 1emv #8 --- PO4 — phosphate ion > view > select #8/A:71 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 121 atoms, 123 bonds, 16 residues, 1 model selected > select up 651 atoms, 664 bonds, 83 residues, 1 model selected > delete sel > mmaker #8/B:100-110 to #6/Aa:300-310 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 halfcleaved_HNH_center_main_model_refined_with_water.pdb, chain Aa (#6) with 1emv, chain B (#8), sequence alignment score = 35.4 RMSD between 9 pruned atom pairs is 0.264 angstroms; (across all 9 pairs: 0.264) > view > show #!6 models > hide #!6 models > show #!6 models > hide #8 models > show #8 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > select #8/B:127 10 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > show #!6 models > hide #!6 models > show #!6 models > select #8/B:100 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > hide #8 models > hide #!6 models > show #!5 models > hide #!5 models > show #!2 models > show #!6 models > select #6/Aa:303 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > select #2/E:704 8 atoms, 7 bonds, 1 residue, 1 model selected > select #6/Aa:306 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/E:706 7 atoms, 7 bonds, 1 residue, 1 model selected > select #6/Ba:128 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!4 models > lighting simple > lighting soft > lighting simple > hide #!4 models > hide #!2 models > hide #!6 models > show #8 models > set chain Expected a keyword > set chain #8/B A Expected a keyword > set chain #8/B to A Expected a keyword > set chain A #8/B Expected a keyword > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_refined2.pdb"" Chain information for halfcleaved_HNH_center_main_model_refined2.pdb #9 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available > color #9/L light gray > color #9/K dim gray > color #9/J dark red > color #9/I rebecca purple > color #9/B forest green > color #9/C,D,E,F,G,H khaki > color #9/A steel blue > color #9/A:232-350 dark turquoise > style stick Changed 106889 atom styles > hide #9 atoms > show #9 cartoons > hide #!9 models > show #!3 models > hide #!3 models > show #!6 models > hide #!6 models > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > hide #8 models > show #8 models > hide #8 models > show #8 models > hide #8 models > show #8 models > show #9/M atoms > show #9/N atoms > hide #!9 models > show #!9 models > hide #8 models > show #8 models > hide #8 models > hide #!9 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"" Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #10 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available > hide #10 atoms > show #10 cartoons > cartoon style nucleic xsection oval width 1.6 thickness 1.6 > color #10/L light gray > color #10/K dim gray > color #10/J dark red > color #10/I rebecca purple > color #10/B forest green > color #10/C,D,E,F,G,H khaki > color #10/A steel blue > color #10/A:232-350 dark turquoise > show #10/K atoms > style stick Changed 131055 atom styles > show #10 & nucleic atoms > select #10 24166 atoms, 24925 bonds, 3 pseudobonds, 2803 residues, 2 models selected > nucleotides sel ladder > select clear > show #!4 models > volume #4 level 0.06 > show #10/M,N,O atoms > select clear > select #10/K:4 4 atoms, 3 bonds, 1 residue, 1 model selected > select add #10/K:3 25 atoms, 26 bonds, 2 residues, 1 model selected > select add #10/K:2 45 atoms, 47 bonds, 3 residues, 1 model selected > select add #10/K:1 54 atoms, 56 bonds, 4 residues, 1 model selected > hide sel cartoons > nucleotides sel atoms > style nucleic & sel stick Changed 54 atom styles > select clear > color zone #4 near #10 distance 10 > transparency 50 > volume #4 level 0.05 > cartoon style nucleic xsection oval width 1 thickness 1 > color #10/L light gray > color #10/K dim gray > color #10/J dark red > color #10/I rebecca purple > color #10/B forest green > color #10/C,D,E,F,G,H khaki > color #10/A steel blue > color #10/A:232-350 dark turquoise > color zone #4 near #10 distance 10 > hide #!10 models > hide #!4 models > show #!10 models > select #10/M:1@MG 1 atom, 1 residue, 1 model selected > color sel red > select #10/O:1@O 1 atom, 1 residue, 1 model selected > color sel blue > select clear > color zone #4 near #10 distance 10 > show #!4 models > hide #!10 models > color zone #4 near #10 distance 5 > volume #4 level 0.09 > lighting soft > lighting full > lighting soft > color zone #4 near #10 distance 4 > color zone #4 near #10 distance 3 > volume #4 level 0.07 > surface zone #4 nearAtoms #10 distance 2.5 > surface zone #4 nearAtoms #10 distance 3 > select add #4 2 models selected > ui tool show ""Color Actions"" > color sel navajo white > set bgColor white > lighting simple > transparency sel 50 > show #!10 models > volume #4 level 0.05 > volume #4 level 0.09 > volume #4 level 0.08 > color #10 byhetero > select clear > select #10/K:1@N9 1 atom, 1 residue, 1 model selected > select up 9 atoms, 9 bonds, 1 residue, 1 model selected > select add #10/K:2@OP2 10 atoms, 9 bonds, 2 residues, 1 model selected > select up 29 atoms, 31 bonds, 2 residues, 1 model selected > select down 10 atoms, 9 bonds, 2 residues, 1 model selected > select add #10/K:2@OP1 11 atoms, 12 bonds, 2 residues, 1 model selected > select add #10/K:2@O2 12 atoms, 17 bonds, 2 residues, 1 model selected > select add #10/K:2@O4 13 atoms, 20 bonds, 2 residues, 1 model selected > select add #10/K:2@C5 14 atoms, 21 bonds, 2 residues, 1 model selected > select add #10/K:2@C7 15 atoms, 24 bonds, 2 residues, 1 model selected > select add #10/K:3@N6 16 atoms, 25 bonds, 3 residues, 1 model selected > select up 28 atoms, 27 bonds, 3 residues, 1 model selected > select up 50 atoms, 55 bonds, 3 residues, 1 model selected > hide #!4 models > select subtract #10/K:3@OP1 49 atoms, 53 bonds, 3 residues, 1 model selected > select subtract #10/K:3@P 48 atoms, 51 bonds, 3 residues, 1 model selected > select subtract #10/K:3@OP2 47 atoms, 51 bonds, 3 residues, 1 model selected > select add #10/K:4@P 48 atoms, 51 bonds, 4 residues, 1 model selected > select add #10/K:4@OP1 49 atoms, 52 bonds, 4 residues, 1 model selected > select add #10/K:4@OP2 50 atoms, 54 bonds, 4 residues, 1 model selected > select subtract #10/K:2@O3' 49 atoms, 53 bonds, 4 residues, 1 model selected > select subtract #10/K:2@C4' 48 atoms, 50 bonds, 4 residues, 1 model selected > select subtract #10/K:2@O4' 47 atoms, 48 bonds, 4 residues, 1 model selected > select subtract #10/K:2@C3' 46 atoms, 48 bonds, 4 residues, 1 model selected > select subtract #10/K:2@C2' 45 atoms, 47 bonds, 4 residues, 1 model selected > select subtract #10/K:2@C1' 44 atoms, 46 bonds, 4 residues, 1 model selected > select subtract #10/K:2@C5' 43 atoms, 46 bonds, 4 residues, 1 model selected > hide sel atoms > show #10/K:3 atoms > hide sel atoms > select #10/K:3@C5' 1 atom, 1 residue, 1 model selected > hide sel atoms > select #10/K:3@C4' 1 atom, 1 residue, 1 model selected > select add #10/K:3@O3' 2 atoms, 1 residue, 1 model selected > select add #10/K:3@C2' 3 atoms, 1 residue, 1 model selected > select add #10/K:3@O4' 4 atoms, 1 residue, 1 model selected > hide sel atoms > select #10/K:3@C3' 1 atom, 1 residue, 1 model selected > select add #10/K:3@C1' 2 atoms, 1 residue, 1 model selected > select add #10/K:3@C8 3 atoms, 1 residue, 1 model selected > select up 21 atoms, 23 bonds, 1 residue, 1 model selected > select down 3 atoms, 1 residue, 1 model selected > select add #10/K:3@N3 4 atoms, 1 residue, 1 model selected > select add #10/K:3@C4 5 atoms, 1 residue, 1 model selected > select add #10/K:3@C5 6 atoms, 1 residue, 1 model selected > select add #10/K:3@N7 7 atoms, 1 residue, 1 model selected > select add #10/K:3@C6 8 atoms, 1 residue, 1 model selected > select add #10/K:3@N6 9 atoms, 1 residue, 1 model selected > select add #10/K:3@N1 10 atoms, 1 residue, 1 model selected > select add #10/K:3@C2 11 atoms, 1 residue, 1 model selected > hide sel atoms > select #10/K:3@N9 1 atom, 1 residue, 1 model selected > hide sel atoms > show #!4 models > select #10/K:2@C5' 1 atom, 1 residue, 1 model selected > hide sel atoms > volume #4 level 0.07 > show #10/A:305,304,280,328 > volume #4 level 0.09 > select #10/K:4@O5' 1 atom, 1 residue, 1 model selected > hide sel atoms > color #10/M red > color #10/O blue > color #10/O dark blue > color #10/O blue > volume #4 level 0.07 > show #10/K:2 atoms > volume #4 level 0.06 > show #10/K:1-2 atoms > show #!5 models > hide #!5 models > show #!2 models > hide #!2 models > hide #!4 models > hide #!10 models > show #!10 models > select #10/K:1@O5' 1 atom, 1 residue, 1 model selected > select add #10/K:1@C5' 2 atoms, 1 residue, 1 model selected > select add #10/K:1@C4' 3 atoms, 1 residue, 1 model selected > select add #10/K:1@O4' 4 atoms, 1 residue, 1 model selected > select add #10/K:1@C1' 5 atoms, 1 residue, 1 model selected > select add #10/K:1@N9 6 atoms, 1 residue, 1 model selected > select add #10/K:1@C2' 7 atoms, 1 residue, 1 model selected > select add #10/K:1@C3' 8 atoms, 1 residue, 1 model selected > select add #10/K:1@O3' 9 atoms, 1 residue, 1 model selected > select add #10/K:2@P 10 atoms, 2 residues, 1 model selected > select add #10/K:2@OP2 11 atoms, 2 residues, 1 model selected > select add #10/K:2@OP1 12 atoms, 2 residues, 1 model selected > select add #10/K:2@O5' 13 atoms, 2 residues, 1 model selected > select add #10/K:2@C5' 14 atoms, 2 residues, 1 model selected > hide sel atoms > show #!4 models > hide #!4 models > ui tool show Distances > select #10/O:1@O 1 atom, 1 residue, 1 model selected > select #10/K:3@OP2 1 atom, 1 residue, 1 model selected > select add #10/O:1@O 2 atoms, 2 residues, 1 model selected > distance #10/K:3@OP2 #10/O:1@O Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/K DA 3 OP2 and /O HOH 1 O: 2.479Å > select #10/A:304@ND1 1 atom, 1 residue, 1 model selected > select add #10/M:1@MG 2 atoms, 2 residues, 1 model selected > distance #10/A:304@ND1 #10/M:1@MG Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 304 ND1 and /M MG 1 MG: 2.377Å > select #10/A:328@NE2 1 atom, 1 residue, 1 model selected > select add #10/M:1@MG 2 atoms, 2 residues, 1 model selected > distance #10/A:328@NE2 #10/M:1@MG Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 328 NE2 and /M MG 1 MG: 2.352Å > select #10/M:1@MG 1 atom, 1 residue, 1 model selected > select add #10/K:3@OP1 2 atoms, 2 residues, 1 model selected > distance #10/M:1@MG #10/K:3@OP1 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/M MG 1 MG and /K DA 3 OP1: 3.166Å > select #10/A:280@NH2 1 atom, 1 residue, 1 model selected > select add #10/K:3@OP2 2 atoms, 2 residues, 1 model selected > distance #10/A:280@NH2 #10/K:3@OP2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH2 and /K DA 3 OP2: 2.389Å > select #10/A:280@NH1 1 atom, 1 residue, 1 model selected > select add #10/K:3@O5' 2 atoms, 2 residues, 1 model selected > distance #10/A:280@NH1 #10/K:3@O5' Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A ARG 280 NH1 and /K DA 3 O5': 2.765Å > select #10/A:238 8 atoms, 7 bonds, 1 residue, 1 model selected > select #10/A:319 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #10/A:305@ND1 1 atom, 1 residue, 1 model selected > select add #10/K:3@OP2 2 atoms, 2 residues, 1 model selected > distance #10/A:305@ND1 #10/K:3@OP2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1 and /K DA 3 OP2: 3.592Å > select #10/A:309 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel cartoons > show sel atoms > select #10/A:309@N 1 atom, 1 residue, 1 model selected > select add #10/O:1@O 2 atoms, 2 residues, 1 model selected > distance #10/A:309@N #10/O:1@O Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A LEU 309 N and /O HOH 1 O: 3.104Å > select #10/A:309@N 1 atom, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > show sel cartoons > select clear > view > select #10/A:305@ND1 1 atom, 1 residue, 1 model selected > select add #10/K:3@OP1 2 atoms, 2 residues, 1 model selected > distance #10/A:305@ND1 #10/K:3@OP1 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #10/A HIS 305 ND1 and /K DA 3 OP1: 3.734Å > delete sel > ~distance #10/A:305@ND1 #10/K:3@OP1 > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"" Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #12 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available > style stick Changed 155221 atom styles > hide #12 atoms > color #12/L light gray > color #12/K dim gray > color #12/J dark red > color #12/I rebecca purple > color #12/B forest green > color #12/C,D,E,F,G,H khaki > color #12/A steel blue > color #12/A:232-350 dark turquoise > hide #!11 models > show #!11 models > close #11 > show #12 cartoons > cartoon style nucleic xsection oval width 1 thickness 1 > show #12/K:2-3 atoms > hide #12/K:1-3 cartoons > select clear > select #12/K:2@OP1 1 atom, 1 residue, 1 model selected > select add #12/K:2@OP2 2 atoms, 1 residue, 1 model selected > select add #12/K:2@P 3 atoms, 1 residue, 1 model selected > select add #12/K:2@C5' 4 atoms, 1 residue, 1 model selected > select add #12/K:3@C5' 5 atoms, 2 residues, 1 model selected > select add #12/K:3@C4' 6 atoms, 2 residues, 1 model selected > select add #12/K:3@C3' 7 atoms, 2 residues, 1 model selected > select add #12/K:4 11 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@O4' 12 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@C2' 13 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@C1' 14 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@N9 15 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@C8 16 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@C4 17 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@C5 18 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@N7 19 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@C6 20 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@N6 21 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@N1 22 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@C2 23 atoms, 3 bonds, 3 residues, 1 model selected > select add #12/K:3@N3 24 atoms, 3 bonds, 3 residues, 1 model selected > hide sel atoms > hide sel cartoons > select #12/K:3@O3' 1 atom, 1 residue, 1 model selected > hide sel atoms > select clear > hide #!10 models > show #!10 models > hide #!10 models > show #!10 models > hide #!10 models > select #12/K:2@O5' 1 atom, 1 residue, 1 model selected > hide sel atoms > show #12/M,O atoms > select #12/O:1@O 1 atom, 1 residue, 1 model selected > color sel blue > select #12/M:1@MG 1 atom, 1 residue, 1 model selected > color sel red > select clear > show #12/A:304-305,328,280 > select #12/A:319 8 atoms, 7 bonds, 1 residue, 1 model selected > select ~sel & ##selected 24158 atoms, 24918 bonds, 3 pseudobonds, 2802 residues, 2 models selected > show #12/A:304-305,328,280,319 > color #12 byhetero > select #12/O:1@O 1 atom, 1 residue, 1 model selected > select add #12/M:1@MG 2 atoms, 2 residues, 1 model selected > select #12/M:1@MG 1 atom, 1 residue, 1 model selected > select #12/O:1@O 1 atom, 1 residue, 1 model selected > color sel blue > select #12/M:1@MG 1 atom, 1 residue, 1 model selected > color sel red > select clear > select #12/A:305@ND1 1 atom, 1 residue, 1 model selected > select add #12/K:3@OP2 2 atoms, 2 residues, 1 model selected > distance #12/A:305@ND1 #12/K:3@OP2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 305 ND1 and /K DA 3 OP2: 3.159Å > select #12/A:280@NH2 1 atom, 1 residue, 1 model selected > select add #12/K:3@OP2 2 atoms, 2 residues, 1 model selected > distance #12/A:280@NH2 #12/K:3@OP2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH2 and /K DA 3 OP2: 2.389Å > select #12/A:280@NH1 1 atom, 1 residue, 1 model selected > select add #12/K:3@O5' 2 atoms, 2 residues, 1 model selected > distance #12/A:280@NH1 #12/K:3@O5' Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A ARG 280 NH1 and /K DA 3 O5': 2.765Å > view > select #12/K:3@OP1 1 atom, 1 residue, 1 model selected > select add #12/M:1@MG 2 atoms, 2 residues, 1 model selected > distance #12/K:3@OP1 #12/M:1@MG Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP1 and /M MG 1 MG: 3.166Å > select #12/M:1@MG 1 atom, 1 residue, 1 model selected > select add #12/A:304@ND1 2 atoms, 2 residues, 1 model selected > distance #12/M:1@MG #12/A:304@ND1 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/M MG 1 MG and /A HIS 304 ND1: 2.377Å > select #12/A:328@NE2 1 atom, 1 residue, 1 model selected > select add #12/M:1@MG 2 atoms, 2 residues, 1 model selected > distance #12/A:328@NE2 #12/M:1@MG Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A HIS 328 NE2 and /M MG 1 MG: 2.352Å > select clear > color sel maroon > color sel teal > color sel cornflower blue > color sel dark salmon > color sel dark khaki > color sel peru > select #12/O:1@O 1 atom, 1 residue, 1 model selected > select add #12/K:3@OP2 2 atoms, 2 residues, 1 model selected > color sel indigo > color sel red > select #12/O:1@O 1 atom, 1 residue, 1 model selected > color sel blue > select #12/K:3@OP2 1 atom, 1 residue, 1 model selected > select add #12/O:1@O 2 atoms, 2 residues, 1 model selected > distance #12/K:3@OP2 #12/O:1@O Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/K DA 3 OP2 and /O HOH 1 O: 2.479Å > color sel indigo > select clear > color sel dark blue > select clear > select #12/A:309 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #12/O:1@O 9 atoms, 7 bonds, 2 residues, 1 model selected Exactly two atoms must be selected! > select clear > select #12/A LEU 309 N Expected a keyword > select #12/A:309 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > select #12/A:309@N 1 atom, 1 residue, 1 model selected > select add #12/O:1@O 2 atoms, 2 residues, 1 model selected > distance #12/A:309@N #12/O:1@O Distance between halfcleaved_HNH_center_main_model_temp2.pdb #12/A LEU 309 N and /O HOH 1 O: 3.104Å > distance style decimalPlaces 2 > distance style decimalPlaces 1 > select subtract #12/O:1@O 1 atom, 1 residue, 1 model selected > select ~sel & ##selected 24165 atoms, 24925 bonds, 11 pseudobonds, 2803 residues, 3 models selected > hide #12/A:309 atoms > show #12/A:309 cartoons > select clear > show #!4 models > volume #4 level 0.07 > volume #4 level 0.08 > select #12/K:2@N3 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 886 atoms, 986 bonds, 45 residues, 1 model selected > select down 20 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms > surface dust #4 size 7.25 > surface dust #4 1 Expected a keyword > surface dust #4 size 1 > show (sel-residues & sidechain) target ab > hide sel atoms > select clear > select #12/K:3@O5' 1 atom, 1 residue, 1 model selected > select up 21 atoms, 23 bonds, 1 residue, 1 model selected > show #12/K:2 atoms > select #12/K:2@C2 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > hide #!4 models > select subtract #12/K:2@O3' 19 atoms, 20 bonds, 1 residue, 1 model selected > hide sel atoms > show #!4 models > volume #4 level 0.06 > volume #4 level 0.08 > volume #4 level 0.09 > volume #4 level 0.08 > view matrix models > #12,0.95038,0.072866,-0.30245,40.949,-0.29386,-0.10887,-0.94963,361.72,-0.10212,0.99138,-0.082056,19.143 > show #!10 models > hide #!10 models > mmaker #12 to #10 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 halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#10) with halfcleaved_HNH_center_main_model_temp2.pdb, chain A (#12), sequence alignment score = 1753 RMSD between 340 pruned atom pairs is 0.001 angstroms; (across all 340 pairs: 0.001) > ui tool show ""Side View"" > hide #11.1 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif"" width 1984 height > 1210 supersample 3 transparentBackground true > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > select #2/E:804@O1 1 atom, 1 residue, 1 model selected > select up 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #2/E:731@CG 6 atoms, 4 bonds, 2 residues, 1 model selected > select up 15 atoms, 14 bonds, 2 residues, 1 model selected > select up 17 atoms, 15 bonds, 3 residues, 1 model selected > select up 19 atoms, 16 bonds, 4 residues, 1 model selected > select add #12/A:319@OD1 20 atoms, 16 bonds, 5 residues, 2 models selected > select up 39 atoms, 35 bonds, 5 residues, 2 models selected > select add #2/E:31@O 40 atoms, 35 bonds, 6 residues, 2 models selected > select add #2/E:298@O 41 atoms, 35 bonds, 7 residues, 2 models selected > select subtract #2/E:298@O 40 atoms, 35 bonds, 6 residues, 2 models selected > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > show #2.1 models > hide #2.1 models > select add #12 24198 atoms, 24953 bonds, 11 pseudobonds, 2808 residues, 4 models selected > select subtract #12 32 atoms, 28 bonds, 5 residues, 1 model selected > hide sel atoms > select #2/E:701@CB 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #12/A:319@OD1 1 atom, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select #2/E:298@O 1 atom, 1 residue, 1 model selected > hide sel atoms > color sel dark blue > select clear > show #!4 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif"" width 1984 height > 1210 supersample 3 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > hide #!12 models > hide #!4 models > show #!2 models > select #2/E:904@ZN 1 atom, 1 residue, 1 model selected > hide sel atoms > select clear > hide #!2 models > show #!12 models > select #12/M:1@MG 1 atom, 1 residue, 1 model selected > color sel silver > color sel metallic Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel dark gray > color sel dim gray > select clear > color sel red > select #12/M:1@MG 1 atom, 1 residue, 1 model selected > color sel red > color sel dim gray > select clear > show #!2 models > hide #!2 models > show #!4 models > color sel red > color #12/M red > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif"" width 1984 height > 1210 supersample 3 > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!4 models > color sel tan > color sel dim gray > show #!4 models > select clear > hide #!2 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif"" width 1984 height > 1210 supersample 3 > hide #!4 models > show #!2 models > hide #!11 models > color #2 yellow > sle #2/E Unknown command: sle #2/E > select #2/E 1109 atoms, 1075 bonds, 4 pseudobonds, 190 residues, 2 models selected > select clear > ui tool show ""Show Sequence Viewer"" > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > hide #!2 models > open ""/Users/zxc755/Library/CloudStorage/OneDrive- > UniversityofCopenhagen/Type > I-F_HNH/Manuscript/halfcleaved_HNH_center_main_model_temp2.pdb"" Chain information for halfcleaved_HNH_center_main_model_temp2.pdb #13 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available > hide #13 atoms > show #13 cartoons > cartoon style nucleic xsection oval width 1 thickness 1 > color #13/DA light gray > color #13/EA dim gray > color #13/FA dark red > color #13/Ca rebecca purple > color #13/Ba forest green > color #13/Da,Db,Dc,Dd,De,Df khaki > color #13/Aa steel blue > color #13/Aa:232-350 dark turquoise > hide #!12 models > show #!12 models > hide #!13 models > show #!13 models > hide #!13 models > show #!13 models > color #13/L light gray > color #13/K dim gray > color #13/J dark red > color #13/I rebecca purple > color #13/B forest green > color #13/C,D,E,F,G,H khaki > color #13/A steel blue > color #13/A:232-350 dark turquoise > color #13 byhetero > hide #!12 models > color #13/M red > show #13/K:2 atoms > style stick Changed 179387 atom styles > select #13/K:3 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #13/K:4 25 atoms, 26 bonds, 2 residues, 1 model selected > select add #13/K:2 45 atoms, 47 bonds, 3 residues, 1 model selected > hide sel cartoons > show #13/K:3 atoms > select subtract #13/K:3@O5' 44 atoms, 45 bonds, 3 residues, 1 model selected > select subtract #13/K:3@OP2 43 atoms, 44 bonds, 3 residues, 1 model selected > select subtract #13/K:3@OP1 42 atoms, 43 bonds, 3 residues, 1 model selected > select subtract #13/K:2@O3' 41 atoms, 42 bonds, 3 residues, 1 model selected > select subtract #13/K:2@C3' 40 atoms, 40 bonds, 3 residues, 1 model selected > select add #13/K:2@C3' 41 atoms, 40 bonds, 3 residues, 1 model selected > select subtract #13/K:2@C3' 40 atoms, 40 bonds, 3 residues, 1 model selected > select add #13/K:2@C3' 41 atoms, 40 bonds, 3 residues, 1 model selected > hide sel atoms > select #13/K:2@O3' 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > select up 886 atoms, 986 bonds, 45 residues, 1 model selected > show sel atoms > select #13/K:4@O5' 1 atom, 1 residue, 1 model selected > select add #13/K:4@OP1 2 atoms, 1 residue, 1 model selected > select add #13/K:3@O3' 3 atoms, 2 residues, 1 model selected > select up 25 atoms, 27 bonds, 2 residues, 1 model selected > select subtract #13/K:3@O5' 24 atoms, 25 bonds, 2 residues, 1 model selected > select subtract #13/K:3@P 23 atoms, 23 bonds, 2 residues, 1 model selected > select subtract #13/K:3@OP1 22 atoms, 23 bonds, 2 residues, 1 model selected > select subtract #13/K:3@OP2 21 atoms, 23 bonds, 2 residues, 1 model selected > hide sel atoms > select up 23 atoms, 24 bonds, 3 residues, 1 model selected > select up 45 atoms, 49 bonds, 3 residues, 1 model selected > select down 23 atoms, 24 bonds, 3 residues, 1 model selected > select #13/K:2@N1 1 atom, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > select subtract #13/K:2@O3' 19 atoms, 20 bonds, 1 residue, 1 model selected > hide sel atoms > show #13/A:304-305,328,280 > show #13/M,O > select #13/O:1@O 1 atom, 1 residue, 1 model selected > color sel blue > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!12 models > hide #!12 models > show #!4 models > show #!12 models > hide #!12 models > select #13/K:1 9 atoms, 9 bonds, 1 residue, 1 model selected > hide sel cartoons > select #13/K:1@O5' 1 atom, 1 residue, 1 model selected > select add #13/K:1@C5' 2 atoms, 1 residue, 1 model selected > hide sel atoms > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select Mg 6 atoms, 6 residues, 6 models selected > select Zn 5 atoms, 5 residues, 2 models selected > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > select add #2 4547 atoms, 4317 bonds, 16 pseudobonds, 856 residues, 3 models selected > select subtract #2 1 atom, 1 residue, 1 model selected > hide #!4 models > select add #5 6 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected > select subtract #5 Nothing selected > select add #5 6 atoms, 4 bonds, 1 pseudobond, 2 residues, 2 models selected > select subtract #5 Nothing selected > hide #!5 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select Zn 5 atoms, 5 residues, 2 models selected > select add #5 10 atoms, 4 bonds, 1 pseudobond, 6 residues, 3 models selected > select subtract #5 4 atoms, 4 residues, 1 model selected > show sel atoms > show #!2 models > select water Expected an objects specifier or a keyword > ui tool show ""Check Waters"" > hbonds #13/O interModel false reveal true restrict any name ""water H-bonds"" The following atoms were skipped as donors/acceptors due to missing heavy-atom bond partners: halfcleaved_HNH_center_main_model_temp2.pdb #13/K DG 1 N9 2 hydrogen bonds found > show #4 models > select #13/O 1 atom, 1 residue, 1 model selected > display #13/O : view #13/O @ select add #13/K:3@N7 2 atoms, 2 residues, 1 model selected > select up 22 atoms, 23 bonds, 2 residues, 1 model selected > hide #!2 models > hide #!4 models > select subtract #13/K:3@O5' 21 atoms, 21 bonds, 2 residues, 1 model selected > select subtract #13/K:3@OP2 20 atoms, 20 bonds, 2 residues, 1 model selected > select subtract #13/K:3@OP1 19 atoms, 19 bonds, 2 residues, 1 model selected > hide sel atoms > select #13/K:3@O5' 1 atom, 1 residue, 1 model selected > select up 21 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 21 atoms, 23 bonds, 1 residue, 1 model selected > select subtract #13/K:3@P 20 atoms, 20 bonds, 1 residue, 1 model selected > select subtract #13/K:3@OP1 19 atoms, 20 bonds, 1 residue, 1 model selected > select subtract #13/K:3@OP2 18 atoms, 20 bonds, 1 residue, 1 model selected > select subtract #13/K:3@O5' 17 atoms, 19 bonds, 1 residue, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 20 atoms, 21 bonds, 1 residue, 1 model selected > select subtract #13/K:2@O3' 19 atoms, 20 bonds, 1 residue, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 9 atoms, 9 bonds, 1 residue, 1 model selected > hide sel atoms > select #13/A:308@CD 1 atom, 1 residue, 1 model selected > select up 7 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > hide sel cartoons > select #13/A:309@N 1 atom, 1 residue, 1 model selected > show #13/O atoms > show #!11 models > hide #!11 models > close #11 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > show sel cartoons > hide sel > select #13/O:1@O 1 atom, 1 residue, 1 model selected > select add #13/K:3@OP2 2 atoms, 2 residues, 1 model selected > distance #13/O:1@O #13/K:3@OP2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/O HOH 1 O and /K DA 3 OP2: 2.5Å > select #13/A:309 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > hide sel cartoons > show sel atoms > select #13/A:309@N 1 atom, 1 residue, 1 model selected > select add #13/O:1@O 2 atoms, 2 residues, 1 model selected > distance #13/A:309@N #13/O:1@O Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A LEU 309 N and /O HOH 1 O: 3.1Å > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 8 atoms, 7 bonds, 1 residue, 1 model selected > hide sel atoms > show sel cartoons > hide #11.1 models > select #13/M:2@MG 1 atom, 1 residue, 1 model selected > select add #13/K:2@O3' 2 atoms, 2 residues, 1 model selected > distance #13/M:2@MG #13/K:2@O3' Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/M MG 2 MG and /K DT 2 O3': 2.9Å > select #13/A:304@ND1 1 atom, 1 residue, 1 model selected > select add #13/M:2@MG 2 atoms, 2 residues, 1 model selected > distance #13/A:304@ND1 #13/M:2@MG Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 304 ND1 and /M MG 2 MG: 2.6Å > select #13/A:328@NE2 1 atom, 1 residue, 1 model selected > select add #13/M:2@MG 2 atoms, 2 residues, 1 model selected > distance #13/A:328@NE2 #13/M:2@MG Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 328 NE2 and /M MG 2 MG: 2.0Å > select clear > select #13/A:305@ND1 1 atom, 1 residue, 1 model selected > select add #13/K:3@OP2 2 atoms, 2 residues, 1 model selected > distance #13/A:305@ND1 #13/K:3@OP2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/A HIS 305 ND1 and /K DA 3 OP2: 3.2Å > select #13/K:3@O5' 1 atom, 1 residue, 1 model selected > select add #13/A:280@NH1 2 atoms, 2 residues, 1 model selected > distance #13/K:3@O5' #13/A:280@NH1 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 O5' and /A ARG 280 NH1: 2.8Å > select #13/K:3@OP2 1 atom, 1 residue, 1 model selected > select add #13/A:280@NH2 2 atoms, 2 residues, 1 model selected > distance #13/K:3@OP2 #13/A:280@NH2 Distance between halfcleaved_HNH_center_main_model_temp2.pdb #13/K DA 3 OP2 and /A ARG 280 NH2: 2.4Å > select add #11 8 pseudobonds, 2 models selected > color sel dim gray > show #!2 models > hide #!2 models > show #!4 models > unsel Unknown command: unsel > select 179387 atoms, 183813 bonds, 57 pseudobonds, 19979 residues, 49 models selected > select clear > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_0p8.tif"" width 1984 height > 1210 supersample 3 > show #!2 models > hide #!4 models > hide #!11 models > select #2/E:31@O 1 atom, 1 residue, 1 model selected > hide sel atoms > select clear > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif"" width 1984 height > 1210 supersample 3 > lighting soft > show #!4 models > hide #!2 models > lighting full > lighting simple > lighting full > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > lighting simple > show #!2 models > hide #!4 models > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/structure/HNH/HNH_cat_1fsj.tif"" width 1984 height > 1210 supersample 3 > hide #!2 models > show #!4 models > hide #!4 models > show #!4 models > volume #4 level 0.09 > volume #4 level 0.1 > volume #4 level 0.95 > volume #4 level 0.095 > volume #4 level 0.09 > volume #4 level 0.08 > volume #4 level 0.09 > select #13/K:6 22 atoms, 24 bonds, 1 residue, 1 model selected > show #13/L atoms > select clear > show #13/L,J atoms > select clear > save ""/Users/zxc755/OneDrive - University of Copenhagen/Type > I-F_HNH/Manuscript/figures/chimera_session.cxs"" ===== Log before crash end ===== OpenGL version: 4.1 ATI-6.1.13 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2.3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2069.80.3.0.0 (iBridge: 22.16.13060.0.0,0) OS Loader Version: 582~3311 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 6 days, 20 hours, 9 minutes Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 4 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-019 Option ROM Version: 113-D32206U1-019 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 3072 x 1920 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Odyssey G70B: Resolution: 5120 x 2880 (5K/UHD+ - Ultra High Definition Plus) UI Looks like: 2560 x 1440 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: H1AK500000 Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 biopython: 1.84 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 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: 1.2.2 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-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 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: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 DiffFit: 0.2 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 fsspec: 2024.6.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 joblib: 1.4.2 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 mpmath: 1.3.0 mrcfile: 1.5.1 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scikit-learn: 1.5.1 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 sympy: 1.13.0 tables: 3.8.0 tcia-utils: 1.5.1 threadpoolctl: 3.5.0 tifffile: 2024.1.30 tinyarray: 1.2.4 torch: 2.2.2 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Window Toolkit duplicate all ChimeraX