id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15630 Crash changing Mac display configuration chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.5-arm64-arm-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 0x00000001eb458c00 (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.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, 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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp, chimerax.alignment_algs._sw (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2024-07-18 11:11:35.00 +0200"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""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 14.5 (23F79)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""AC904530-BA80-4376-B9AC-58D94C13672E""} { ""uptime"" : 260000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 503, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,6"", ""coalitionID"" : 75408, ""osVersion"" : { ""train"" : ""macOS 14.5"", ""build"" : ""23F79"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-07-18 11:11:15.9931 +0200"", ""codeSigningMonitor"" : 1, ""incident"" : ""AC904530-BA80-4376-B9AC-58D94C13672E"", ""pid"" : 27258, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-07-16 10:58:41.8850 +0200"", ""procStartAbsTime"" : 4591749742061, ""procExitAbsTime"" : 6343215777048, ""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"":""C6228A1F-62EF-52B4-877A-D6481F4E4C39"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""43732AE4-1F82-5886-841C-663749D5F8E3"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRW+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkVDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""sleepWakeUUID"" : ""2CDCCEA9-79F8-496F-825F-61EF5D869FA4"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x3def4be8b448 is not in any region. 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(unallocated)\n__AUTH 2199K 404 \n__AUTH_CONST 31.8M 623 \n__CTF 824 1 \n__DATA 22.1M 779 \n__DATA_CONST 42.6M 789 \n__DATA_DIRTY 2024K 232 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 562.5M 161 \n__OBJC_RO 71.9M 1 \n__OBJC_RW 2199K 1 \n__TEXT 938.8M 806 \ndyld private memory 320K 3 \nmapped file 636.9M 105 \nshared memory 3136K 21 \n=========== ======= ======= \nTOTAL 6.2G 5118 \nTOTAL, minus reserved VM space 6.0G 5118 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""8c8ea72d82a1b56be45e2dcc4bffe810610d0f61"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5f72dc58705eff005a46b3a9"", ""factorPackIds"" : { }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""648a2601f74c42732876cb5b"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""667e0061afc7c17197d69e54"" }, ""deploymentId"" : 240000210 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 } ] } } ===== 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 2kzi fromDatabase pdb format mmcif 2kzi title: Solution structure of the ZHER2 Affibody [more info...] Chain information for 2kzi --- Chain | Description 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 1.22/A | Engineered protein, ZHER2 Affibody > set bgColor white > close #1.1-21 > close #1 > open 2kzj fromDatabase pdb format mmcif 2kzj title: Solution structure of the ZHER2 Affibody (alternative) [more info...] Chain information for 2kzj --- Chain | Description 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 1.22/A 1.23/A | Engineered protein, ZHER2 Affibody > close #1.1-22 > color #1.23 #d6d6d6ff > hide #!1 models > hide #1.23 models > open 1ot8 fromDatabase pdb format mmcif 1ot8 title: Structure of the Ankyrin Domain of the Drosophila Notch Receptor [more info...] Chain information for 1ot8 #2 --- Chain | Description | UniProt A B C | Neurogenic locus Notch protein | NOTCH_DROME 2-239 Non-standard residues in 1ot8 #2 --- MG — magnesium ion 1ot8 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 3| author_defined_assembly > color #2 #d6d6d6ff > view orient > hide #!2 atoms > hide #!2 cartoons > select #2/A 1732 atoms, 1590 bonds, 5 pseudobonds, 370 residues, 2 models selected > view orient > close #2.1 > color #2 #d6d6d6ff > ui tool show ""Side View"" > view > view orient > select #2/A 1732 atoms, 1590 bonds, 370 residues, 1 model selected > show sel cartoons > color #2 #d6d6d6ff > hide #2 models > select add #2 5036 atoms, 4623 bonds, 1076 residues, 1 model selected > show #2 models > select subtract #2 Nothing selected > hide #2 models > open 1ttg fromDatabase pdb format mmcif Summary of feedback from opening 1ttg fetched from pdb --- warning | Atom H1 is not in the residue template for VAL /A:1 1ttg title: The three-dimensional structure of the tenth type III module of fibronectin: an insight INTO RGD-mediated interactions [more info...] Chain information for 1ttg #3 --- Chain | Description | UniProt A | FIBRONECTIN | FINC_HUMAN 1-94 > color #3 #d6d6d6ff > graphics silhouettes true > lighting soft > hide #3 models > open 2LUR fromDatabase pdb format mmcif 2lur title: NMR solution structure of Kb1[ghrw;23-28] [more info...] Chain information for 2lur --- Chain | Description 4.1/A 4.2/A 4.3/A 4.4/A 4.5/A 4.6/A 4.7/A 4.8/A 4.9/A 4.10/A 4.11/A 4.12/A 4.13/A 4.14/A 4.15/A 4.16/A 4.17/A 4.18/A 4.19/A 4.20/A | Kalata > close #4.1-19 > color #4.20 #d6d6d6ff > hide #!4 models > hide #4.20 models > show #4.20 models > hide #!4 models > show #1.23 models > hide #!1 models > open 8AJ7 fromDatabase pdb format mmcif 8aj7 title: Kunitz domain of Amblyomin-X [more info...] Chain information for 8aj7 #5 --- Chain | Description A B | Kunitz domain of Amblyomin-X Non-standard residues in 8aj7 #5 --- EDO — 1,2-ethanediol (ethylene glycol) 8aj7 mmCIF Assemblies --- 1| author_defined_assembly 2| author_defined_assembly 55 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select #5/A 502 atoms, 461 bonds, 109 residues, 1 model selected > hide sel cartoons > hide sel atoms > color #5 #d6d6d6ff > hide #5 models > select add #5 1010 atoms, 919 bonds, 227 residues, 1 model selected > open 4MVK fromDatabase pdb format mmcif 4mvk title: Crystal structure of an engineered lipocalin (Anticalin US7) in complex with the Alzheimer amyloid peptide fragment VFFAED [more info...] Chain information for 4mvk #6 --- Chain | Description | UniProt A | Neutrophil gelatinase-associated lipocalin | NGAL_HUMAN 1-178 B | Amyloid peptide fragment VFFAED | A4_HUMAN 18-23 Non-standard residues in 4mvk #6 --- ACE — acetyl group NH2 — amino group > hide #6 atoms > select subtract #5 Nothing selected > show #!1 models > show #2 models > show #3 models > show #!4 models > show #5 models > tile 6 models tiled > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting simple > lighting soft > hide #!1 models > hide #2 models > hide #3 models > hide #!4 models > hide #5 models > hide #6 models > show #2 models > hide #2 models > show #!1 models > show #2 models > show #3 models > show #!4 models > show #5 models > show #6 models > hide #!1 models > hide #2 models > hide #3 models > hide #!4 models > hide #5 models > hide #6 models > show #3 models > hide #3 models > show #!4 models > hide #!4 models > show #5 models > hide #5 models > show #6 models > show #5 models > show #!4 models > show #3 models > show #2 models > show #!1 models > save /Users/annamb/Desktop/image1.png supersample 3 > save /Users/annamb/Desktop/image2.png supersample 3 > save /Users/annamb/Desktop/PhD-220727/Thesis/Alternative-scaffolds.cxs > open 6ARP fromDatabase pdb format mmcif Summary of feedback from opening 6ARP fetched from pdb --- note | Fetching compressed mmCIF 6arp from http://files.rcsb.org/download/6arp.cif 6arp title: Structure of a mutant Cetuximab Fab fragment [more info...] Chain information for 6arp #7 --- Chain | Description | UniProt A C | Cetuximab mutant light chain,Uncharacterized protein | Q8TCD0_HUMAN 107-214 B D | Cetuximab mutant Fab heavy chain,Immunoglobulin gamma-1 heavy chain | IGG1_HUMAN 120-222 Non-standard residues in 6arp #7 --- GOL — glycerol (glycerin; propane-1,2,3-triol) SO4 — sulfate ion 6arp mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 172 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > hide #!1 models > hide #2 models > hide #3 models > hide #!4 models > hide #5 models > hide #6 models > close #7.1 > select #7/B 1799 atoms, 1679 bonds, 379 residues, 1 model selected > select #7/B#7/D 3658 atoms, 3388 bonds, 791 residues, 1 model selected > select add #7 7462 atoms, 6757 bonds, 1724 residues, 1 model selected > select subtract #7 Nothing selected > select #7/A 1887 atoms, 1680 bonds, 456 residues, 1 model selected > select #7/B 1799 atoms, 1679 bonds, 379 residues, 1 model selected Drag select of 44 atoms, 227 residues, 34 bonds Drag select of 83 atoms, 612 residues, 65 bonds > select add #7 7462 atoms, 6757 bonds, 1724 residues, 1 model selected > select subtract #7 Nothing selected Drag select of 77 atoms, 431 residues, 61 bonds > select #7/C:27 9 atoms, 8 bonds, 1 residue, 1 model selected Drag select of 77 atoms, 431 residues, 61 bonds > select add #7 7462 atoms, 6757 bonds, 1724 residues, 1 model selected > select subtract #7 Nothing selected Drag select of 180 atoms, 430 residues, 143 bonds > hide sel atoms > hide sel cartoons > hide sel atoms Drag select of 77 atoms, 427 residues, 61 bonds > hide sel atoms > select add #7 7462 atoms, 6757 bonds, 1724 residues, 1 model selected > select subtract #7 Nothing selected > color #7 #d6d6d6ff > select coil 6314 atoms, 6280 bonds, 784 residues, 7 models selected > select add #7 11239 atoms, 10518 bonds, 2157 residues, 7 models selected > select subtract #7 3777 atoms, 3761 bonds, 433 residues, 6 models selected > hide #7 models > show #7 models Alignment identifier is 1.23/A Alignment identifier is 1 Alignment identifier is 3/A Alignment identifier is 4.20/A Alignment identifier is 2 Alignment identifier is 6/A Alignment identifier is 6/B Alignment identifier is 1.23/A Alignment identifier is 1 Alignment identifier is 3/A Alignment identifier is 4.20/A Alignment identifier is 2 Alignment identifier is 6/A Alignment identifier is 6/B > select add #6 4741 atoms, 4603 bonds, 691 residues, 6 models selected > select add #5 5335 atoms, 5108 bonds, 858 residues, 6 models selected > select add #4 5403 atoms, 5180 bonds, 864 residues, 7 models selected > select add #3 6201 atoms, 5994 bonds, 914 residues, 7 models selected > select add #2 9602 atoms, 9005 bonds, 1773 residues, 7 models selected > select add #1 10372 atoms, 9784 bonds, 1820 residues, 8 models selected > select subtract #1 9429 atoms, 8833 bonds, 1762 residues, 6 models selected > select subtract #2 4393 atoms, 4210 bonds, 686 residues, 5 models selected > select subtract #3 2991 atoms, 2792 bonds, 592 residues, 4 models selected > select subtract #4 2608 atoms, 2398 bonds, 563 residues, 2 models selected > select subtract #5 1598 atoms, 1479 bonds, 336 residues, 1 model selected > select subtract #6 Nothing selected Alignment identifier is 1.23/A Alignment identifier is 1 Alignment identifier is 3/A Alignment identifier is 4.20/A Alignment identifier is 2 Alignment identifier is 6/A Alignment identifier is 6/B Alignment identifier is 3 Alignment identifier is 4 > select #7/D,B:61-64,73-75,86-90,162-164,193-195,207-210 316 atoms, 310 bonds, 44 residues, 1 model selected > select > #7/D,B:3-6,10-12,18-25,34-39,45-51,57-59,67-72,77-82,91-98,106-109,113-117,126-130,141-151,157-160,169-171,175-176,182-191,201-206,211-216 1712 atoms, 1724 bonds, 214 residues, 1 model selected > close #7 > open "" 1YYB"" fromDatabase pdb format mmcif PDB identifiers are either 4 or 8 characters long, got "" 1YYB"" > open "" 1YYB"" fromDatabase pdb format mmcif PDB identifiers are either 4 or 8 characters long, got "" 1YYB"" > open 5ESQ fromDatabase pdb format mmcif Summary of feedback from opening 5ESQ fetched from pdb --- notes | Fetching compressed mmCIF 5esq from http://files.rcsb.org/download/5esq.cif Fetching CCD BAL from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/BAL/BAL.cif Fetching CCD PO4 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/4/PO4/PO4.cif 5esq title: Cetuximab Fab in complex with cyclic beta-alanine-linked meditope [more info...] Chain information for 5esq #7 --- Chain | Description A C | Cetuximab Fab light chain B D | Cetuximab Fab heavy chain E F | Cyclic beta-alanine-linked meditope Non-standard residues in 5esq #7 --- BAL — β-alanine PO4 — phosphate ion 5esq mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 54 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > tile 1 model tiled > hide #!7 surfaces > hide #!7 cartoons > show #!7 cartoons > style #!7 stick Changed 7064 atom styles > style #!7 stick Changed 7064 atom styles > style #!7 sphere Changed 7064 atom styles > style #!7 sphere Changed 7064 atom styles > nucleotides #!7 atoms > style nucleic & #!7 stick Changed 0 atom styles > style #!7 ball Changed 7064 atom styles > style #!7 sphere Changed 7064 atom styles > style #!7 sphere Changed 7064 atom styles > style #!7 ball Changed 7064 atom styles > style #!7 stick Changed 7064 atom styles > nucleotides #!7 atoms > style nucleic & #!7 stick Changed 0 atom styles > nucleotides #!7 tube/slab shape box > hide #!7 atoms Drag select of 436 residues, 2 pseudobonds > hide sel cartoons Drag select of 1 residues > hide sel cartoons > select #7/B 1717 atoms, 1681 bonds, 1 pseudobond, 296 residues, 2 models selected > color #7.1 #929292ff models > color #7.1 #919191ff models > color #7 darkgrey > color #7 #5e5e5eff > color #7 #797979ff > color #7 #d6d6d6ff > select add #7.1 1717 atoms, 1681 bonds, 3 pseudobonds, 296 residues, 2 models selected > select add #7 7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected > select subtract #7 Nothing selected Destroying pre-existing alignment with identifier 1.23/A Alignment identifier is 1.23/A Alignment identifier is 3 Destroying pre-existing alignment with identifier 3/A Alignment identifier is 3/A Destroying pre-existing alignment with identifier 4.20/A Alignment identifier is 4.20/A Alignment identifier is 4 Destroying pre-existing alignment with identifier 6/A Alignment identifier is 6/A Destroying pre-existing alignment with identifier 6/B Alignment identifier is 6/B Alignment identifier is 5 Alignment identifier is 6 Alignment identifier is 7 > select #7/B,D:26 8 atoms, 6 bonds, 2 residues, 1 model selected > select #7/B,D:26-30 72 atoms, 72 bonds, 10 residues, 1 model selected > select #7/B,D:52 28 atoms, 30 bonds, 2 residues, 1 model selected > select #7/B,D:52-56 72 atoms, 74 bonds, 10 residues, 1 model selected > select #7/B,D:99 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/B,D:99-108 192 atoms, 200 bonds, 20 residues, 1 model selected > select #7/B,D:52 28 atoms, 30 bonds, 2 residues, 1 model selected > select #7/B,D:52-55 56 atoms, 58 bonds, 8 residues, 1 model selected > select #7/B,D:52-56 72 atoms, 74 bonds, 10 residues, 1 model selected > select #7/B,D:99-108 192 atoms, 200 bonds, 20 residues, 1 model selected > select #7/B,D:52-55 56 atoms, 58 bonds, 8 residues, 1 model selected > select #7/B,D:26 8 atoms, 6 bonds, 2 residues, 1 model selected > select #7/B,D:26-30 72 atoms, 72 bonds, 10 residues, 1 model selected > color sel #ff2600ff > select #7/B,D:52-53 40 atoms, 42 bonds, 4 residues, 1 model selected > select #7/B,D:52-56 72 atoms, 74 bonds, 10 residues, 1 model selected > color sel red > select #7/B,D:99 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/B,D:99-108 192 atoms, 200 bonds, 20 residues, 1 model selected > color sel red > select #7/B,D:26 8 atoms, 6 bonds, 2 residues, 1 model selected > select #7/B,D:26-31 88 atoms, 88 bonds, 12 residues, 1 model selected > color sel blue > select #7/B,D:52-53 40 atoms, 42 bonds, 4 residues, 1 model selected > select #7/B,D:52-56 72 atoms, 74 bonds, 10 residues, 1 model selected > color sel blue > select #7/B,D:99 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/B,D:99-108 192 atoms, 200 bonds, 20 residues, 1 model selected > color sel blue > select #7/A,C:24 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/A,C:24-33 138 atoms, 136 bonds, 20 residues, 1 model selected > color sel medium blue > select #7/A,C:50 24 atoms, 24 bonds, 2 residues, 1 model selected > select #7/A,C:50-55 92 atoms, 92 bonds, 12 residues, 1 model selected > color sel medium blue > select #7/A,C:89 18 atoms, 16 bonds, 2 residues, 1 model selected > select #7/A,C:89-96 140 atoms, 144 bonds, 16 residues, 1 model selected > color sel medium blue > select add #7 7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected > select subtract #7 Nothing selected > color #7 #0433ffff > color #7 #0096ffff > color #7 #0433ffff > color #7 #7a81ffff > undo > save /Users/annamb/Desktop/image2.png supersample 3 > select clear Drag select of 4 residues > select #7/A,C:32 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/A,C:26-32 96 atoms, 94 bonds, 14 residues, 1 model selected > color sel cornflower blue > select add #7 7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected > select subtract #7 Nothing selected > color #7 #0433ffff > color #7 #0433fffa > color #7 #0433ffea > color #7 #0433ffc9 > color #7 #0433ffbf > color #7 #0433ffb4 > color #7 #0433ffab > color #7 #0433ffa3 > color #7 #0433ff9c > color #7 #0433ff99 > color #7 #0433ff98 > color #7 #0433ff96 > color #7 #0433ff92 > color #7 #0433ff8d > color #7 #0433ff89 > color #7 #0433ff87 > color #7 #0433ff86 > color #7 #0433ff84 > color #7 #0433ff7e > color #7 #0433ff7d > color #7 #0433ff7b > color #7 #0433ff7a > color #7 #0433ff78 > color #7 #0433ff76 > color #7 #0433ff75 > undo > color #7 #d6d6d6ff > select #7/B,D:26 8 atoms, 6 bonds, 2 residues, 1 model selected > select #7/B,D:26-30 72 atoms, 72 bonds, 10 residues, 1 model selected > select #7/B,D:26-30,52-56 144 atoms, 146 bonds, 20 residues, 1 model selected > select #7/B,D:26-30,52-56,99-108 336 atoms, 346 bonds, 40 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #0433ffff > color sel #0433fffc > color sel #0433fffb > color sel #0433ffe5 > color sel #0433ffe0 > color sel #0433ffdb > color sel #0433ffd6 > color sel #0433ffd1 > color sel #0433ffcf > color sel #0433ffce > color sel #0433ffcd > color sel #0433ffcc > color sel #0433ffcb > color sel #0433ffca > color sel #0433ffc9 > color sel #0433ffc8 > color sel #0433ffc4 > color sel #0433ffc2 > color sel #0433ffbe > color sel #0433ffba > color sel #0433ffb9 > color sel #0433ffb8 > color sel #0433ffb6 > color sel #0433ffb4 > color sel #0433ffb3 > color sel #0433ffb2 > color sel #0433ffae > color sel #0433ffab > color sel #0433ffa9 > color sel #0433ffa6 > color sel #0433ffa3 > color sel #0433ffa2 > color sel #0433ffa0 > color sel #0433ff9e > color sel #0433ff9d > color sel #0433ff9c > color sel #0433ff9a > color sel #0433ff99 > color sel #0433ff98 > color sel #0433ff97 > color sel #0433ff96 > color sel #0433ff95 > color sel #0433ff91 > color sel #0433ff8f > color sel #0433ff8d > color sel #0433ff8c > color sel #0433ff8b > color sel #0433ff89 > color sel #0433ff88 > color sel #0433ff86 > color sel #0433ff84 > color sel #0433ff83 > color sel #0433ff82 > color sel #0433ff81 > color sel #0433ff80 > color sel #0433ff8a > color sel #0433ff8e > color sel #0433ff91 > color sel #0433ff96 > color sel #0433ff9f > color sel #0433ffa9 > color sel #0433ffae > color sel #0433ffb2 > color sel #0433ffb4 > color sel #0433ffb6 > color sel #0433ffb5 > color sel #0433ffb3 > color sel #0433ffaf > color sel #0433ffa7 > color sel #0433ff9c > color sel #0433ff97 > color sel #0433ff8e > color sel #0433ff89 > color sel #0433ff86 > color sel #0433ff84 > color sel #0433ff83 > color sel #0433ff82 > color sel #0433ff81 > color sel #0433ff80 > color sel #0433ffff > color sel #0433ff7f > select add #7 7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected > select subtract #7 Nothing selected > select #7/A,C:24 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/A,C:24-32 122 atoms, 120 bonds, 18 residues, 1 model selected > select #7/A,C:24-32 122 atoms, 120 bonds, 18 residues, 1 model selected > select #7/A,C:33 16 atoms, 14 bonds, 2 residues, 1 model selected > select #7/A,C:24-33 138 atoms, 136 bonds, 20 residues, 1 model selected > select #7/A,C:24-33,50-56 242 atoms, 240 bonds, 34 residues, 1 model selected > select #7/A,C:24-33,50-56 242 atoms, 240 bonds, 34 residues, 1 model selected > select #7/A,C:24-34,50-56 262 atoms, 262 bonds, 36 residues, 1 model selected > select #7/A,C:24-34,50-56,89-99 446 atoms, 452 bonds, 58 residues, 1 model selected > select #7/A,C:24-34,50-56,89-99 446 atoms, 452 bonds, 58 residues, 1 model selected > select #7/A,C:24-34,50-56,89-99 446 atoms, 452 bonds, 58 residues, 1 model selected > select #7/A,C:24-34,50-56,89-99 446 atoms, 452 bonds, 58 residues, 1 model selected > select #7/A,C:24-34,50-56,89-99 446 atoms, 452 bonds, 58 residues, 1 model selected > color sel #0433ffff > color sel #0433ff7d > select add #7 7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected > select subtract #7 Nothing selected > select #7/A,C:98 22 atoms, 22 bonds, 2 residues, 1 model selected > select #7/A,C:98-99 30 atoms, 30 bonds, 4 residues, 1 model selected > color sel #d6d6d6ff > select add #7 7064 atoms, 6868 bonds, 3 pseudobonds, 1232 residues, 2 models selected > select subtract #7 Nothing selected > save /Users/annamb/Desktop/image3.png supersample 3 Unsupported scale factor (0.000000) detected on Display0 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/annamb/Downloads/g12-scfv.cif ""/Users/annamb/Downloads/a12 > scfv.cif"" ""/Users/annamb/Downloads/zwt scfv.cif"" ""/Users/annamb/Downloads/B8 > scfv.cif"" Summary of feedback from opening /Users/annamb/Downloads/g12-scfv.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Summary of feedback from opening /Users/annamb/Downloads/a12 scfv.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Summary of feedback from opening /Users/annamb/Downloads/zwt scfv.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Summary of feedback from opening /Users/annamb/Downloads/B8 scfv.cif --- warnings | Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Chain information for g12-scfv.cif #8 --- Chain | Description A | No description available B | No description available Chain information for a12 scfv.cif #9 --- Chain | Description A | No description available B | No description available Chain information for zwt scfv.cif #10 --- Chain | Description A | No description available B | No description available Chain information for B8 scfv.cif #11 --- Chain | Description A | No description available B | No description available > hide #!7 models > hide #7.1 models > lighting soft > lighting full > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes false Drag select of 44 residues > lighting full > lighting soft > lighting full > lighting simple > hide #8 models > hide #9 models > hide #10 models > hide #11 models > show #9 models > show #8 models > hide #9 models > select add #8 2560 atoms, 2344 bonds, 334 residues, 4 models selected > select add #9 4729 atoms, 4693 bonds, 618 residues, 4 models selected > select add #10 6983 atoms, 7044 bonds, 911 residues, 4 models selected > select add #11 9205 atoms, 9415 bonds, 1200 residues, 4 models selected > select subtract #10 6904 atoms, 7064 bonds, 900 residues, 3 models selected > select subtract #11 4590 atoms, 4693 bonds, 600 residues, 2 models selected > select subtract #9 2293 atoms, 2344 bonds, 300 residues, 1 model selected > select subtract #8 Nothing selected Drag select of 237 residues > hide sel cartoons Drag select of 2 residues > hide sel cartoons Drag select of 3 residues > hide sel cartoons > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean -0.31, maximum 10.39 To also show corresponding color key, enter the above coulombic command and add key true > undo > hide sel surfaces Drag select of 45 residues Drag select of 58 residues > coulombic sel Using Amber 20 recommended default charges and atom types for standard residues Coulombic values for g12-scfv.cif_A SES surface #8.2: minimum, -11.02, mean -0.52, maximum 11.29 To also show corresponding color key, enter the above coulombic command and add key true > undo > mlp sel Map values for surface ""g12-scfv.cif_A SES surface"": minimum -25.35, mean -5.344, maximum 21.49 To also show corresponding color key, enter the above mlp command and add key true > undo > hide sel surfaces > show sel cartoons > undo Drag select of g12-scfv.cif_A SES surface, 64491 of 65098 triangles, 58 residues > hide sel cartoons > show sel cartoons > hide sel surfaces > show sel cartoons > coulombic sel Coulombic values for g12-scfv.cif_A SES surface #8.2: minimum, -11.02, mean -0.52, maximum 11.29 To also show corresponding color key, enter the above coulombic command and add key true > undo > show sel cartoons > hide sel surfaces > mlp Map values for surface ""g12-scfv.cif_A SES surface"": minimum -25.74, mean -5.336, maximum 21.68 Map values for surface ""g12-scfv.cif_B SES surface"": minimum -31.49, mean -7.968, maximum 21.93 Map values for surface ""1ot8_A SES surface"": minimum -28.65, mean -5.892, maximum 21.99 Map values for surface ""1ot8_B SES surface"": minimum -30.87, mean -5.953, maximum 22.58 Map values for surface ""1ot8_C SES surface"": minimum -28.35, mean -6.257, maximum 22.53 Map values for surface ""2kzj_A SES surface"": minimum -22.95, mean -3.088, maximum 24.28 Map values for surface ""2lur_A SES surface"": minimum -29.24, mean -3.03, maximum 23.4 Map values for surface ""1ttg_A SES surface"": minimum -26.79, mean -3.597, maximum 24.88 Map values for surface ""8aj7_A SES surface"": minimum -27.38, mean -6.131, maximum 19.71 Map values for surface ""8aj7_B SES surface"": minimum -24.39, mean -6.308, maximum 18.93 Map values for surface ""5esq_A SES surface"": minimum -27.12, mean -7.066, maximum 22.84 Map values for surface ""5esq_B SES surface"": minimum -31.19, mean -5.59, maximum 22.58 Map values for surface ""5esq_C SES surface"": minimum -29.43, mean -7.12, maximum 22.82 Map values for surface ""5esq_D SES surface"": minimum -30.44, mean -5.523, maximum 22.3 Map values for surface ""5esq_E SES surface"": minimum -22.98, mean -2.931, maximum 22.4 Map values for surface ""5esq_F SES surface"": minimum -28.34, mean 9.21, maximum 120.1 Map values for surface ""4mvk_A SES surface"": minimum -25.36, mean -4.806, maximum 21.44 Map values for surface ""4mvk_B SES surface"": minimum -24.34, mean -3.061, maximum 22.37 Map values for surface ""a12 scfv.cif_A SES surface"": minimum -26.74, mean -4.741, maximum 22.4 Map values for surface ""a12 scfv.cif_B SES surface"": minimum -30.71, mean -7.968, maximum 22.05 Map values for surface ""B8 scfv.cif_A SES surface"": minimum -26.49, mean -4.081, maximum 21.48 Map values for surface ""B8 scfv.cif_B SES surface"": minimum -31.1, mean -8, maximum 23.07 Map values for surface ""zwt scfv.cif_A SES surface"": minimum -25.59, mean -5.122, maximum 21.77 Map values for surface ""zwt scfv.cif_B SES surface"": minimum -29.5, mean -7.889, maximum 22.17 > hide #7.2 models > hide #7.3 models > hide #7.4 models > hide #7.5 models > hide #7.6 models > hide #7.7 models > select add #8 2293 atoms, 2344 bonds, 300 residues, 2 models selected > select subtract #8 2 models selected > hide #2.3 models > hide #2.2 models > hide #2.1 models > show #!8 cartoons > hide #!8 surfaces Drag select of 241 residues Drag select of 232 residues > hide sel cartoons Drag select of 2 residues Drag select of 6 residues > hide sel cartoons > select #8/B:101 12 atoms, 12 bonds, 1 residue, 1 model selected Drag select of 2 residues > hide sel cartoons Drag select of 2 residues > hide sel cartoons > color (#!8 & sel) byhetero > coulombic sel Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean -0.31, maximum 10.39 To also show corresponding color key, enter the above coulombic command and add key true > coulombic sel Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean -0.31, maximum 10.39 To also show corresponding color key, enter the above coulombic command and add key true > undo > hide sel surfaces Drag select of 58 residues > show sel atoms > mlp sel Map values for surface ""g12-scfv.cif_A SES surface"": minimum -25.52, mean -5.35, maximum 22.03 To also show corresponding color key, enter the above mlp command and add key true > hide sel surfaces > color (#!8 & sel) byelement > undo > ui tool show ""Color Actions"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color sel bychain > color sel byhetero > color sel byelement > color sel bynucleotide > hide #!8 models > select add #8 2293 atoms, 2344 bonds, 300 residues, 2 models selected > show #!8 models > hide sel cartoons > show sel cartoons > hbonds sel reveal true 584 hydrogen bonds found > hide sel atoms > show sel atoms > select subtract #8 2 models selected Drag select of 985 atoms, 232 residues, 832 bonds, 192 pseudobonds > select subtract #8/B:184@CD2 1750 atoms, 830 bonds, 192 pseudobonds, 232 residues, 3 models selected > select #8/B:184@CD2 1 atom, 1 residue, 1 model selected Drag select of 877 atoms, 212 residues, 738 bonds, 171 pseudobonds > hide sel atoms > undo > hbonds /a:nad restrict cross log true reveal true Atom specifier selects no atoms > delete solvent > hide protein > hbonds sidechain restrict both reveal true color yellow radius .08 593 hydrogen bonds found > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 139 hydrogen bonds found > coulombic sel Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean -0.31, maximum 10.39 To also show corresponding color key, enter the above coulombic command and add key true > mlp sel Map values for surface ""g12-scfv.cif_B SES surface"": minimum -31.29, mean -7.972, maximum 21.71 To also show corresponding color key, enter the above mlp command and add key true > coulombic sel Coulombic values for g12-scfv.cif_B SES surface #8.1: minimum, -15.15, mean -0.31, maximum 10.39 To also show corresponding color key, enter the above coulombic command and add key true > hide sel surfaces > color #8.1 #ff2600ff > color #8.2 #0433ffff > hide #!8 models > hide #7.8 models > show #!8 models > select add #8 2293 atoms, 2344 bonds, 57 pseudobonds, 300 residues, 4 models selected > select subtract #8 2 models selected > color #8 #941100ff > color #8.2 #0433ffff > select add #8.2 460 atoms, 58 residues, 1 model selected > select subtract #8.2 1 model selected > hide #!8 models > select add #8.1 1833 atoms, 242 residues, 1 model selected > show #!8 models > color #8.1 #0022a7ff > color (#!8 & sel) blue > select subtract #8.1 1 model selected Drag select of 247 atoms, 210 residues, 211 bonds, 36 pseudobonds > hide sel atoms > select subtract #8.1 1 model selected > hide #!8 models > show #!10 models > hide #!10 surfaces > hide #!10 models Alignment identifier is 1.23/A Alignment identifier is 1 Alignment identifier is 3/A Alignment identifier is 4.20/A Alignment identifier is 2 Alignment identifier is 6/A Alignment identifier is 6/B Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 5 Alignment identifier is 8/A Alignment identifier is 6 Alignment identifier is 9/A Alignment identifier is 10/A Alignment identifier is 11/A > select #10/A:1 7 atoms, 6 bonds, 1 residue, 1 model selected > select #10/A 468 atoms, 475 bonds, 7 pseudobonds, 58 residues, 3 models selected > select #10/A:58 9 atoms, 8 bonds, 1 residue, 1 model selected > select #10/A 468 atoms, 475 bonds, 7 pseudobonds, 58 residues, 3 models selected > select #9/A:1 7 atoms, 6 bonds, 1 residue, 1 model selected > select #9/A 464 atoms, 473 bonds, 6 pseudobonds, 58 residues, 3 models selected > select #8/A:1 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A 460 atoms, 468 bonds, 7 pseudobonds, 58 residues, 3 models selected Alignment identifier is 8/A > show #!11 models Alignment identifier is 8/A > hide #8.1 models > hide #8.2 models > hide #10.1 models > hide #10.2 models > hide #!11 models > hide #12 models > hide #13 models > show #!11 models > select add #12 460 atoms, 468 bonds, 594 pseudobonds, 58 residues, 4 models selected > select add #13 460 atoms, 468 bonds, 732 pseudobonds, 58 residues, 4 models selected > select subtract #12 460 atoms, 468 bonds, 139 pseudobonds, 58 residues, 3 models selected > select subtract #13 460 atoms, 468 bonds, 58 residues, 2 models selected > select add #8 2293 atoms, 2344 bonds, 57 pseudobonds, 300 residues, 4 models selected > select subtract #8 2 models selected > select add #8.1 1833 atoms, 242 residues, 1 model selected > select subtract #8.1 1 model selected Alignment identifier is 1.23/A Alignment identifier is 1 Alignment identifier is 3/A Alignment identifier is 4.20/A Alignment identifier is 2 Alignment identifier is 6/A Alignment identifier is 6/B Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 5 Alignment identifier is 8/A Alignment identifier is 6 Alignment identifier is 9/A Alignment identifier is 10/A Alignment identifier is 11/A > select #11/A:1 7 atoms, 6 bonds, 1 residue, 1 model selected > select #11/A 481 atoms, 495 bonds, 8 pseudobonds, 58 residues, 3 models selected > hide sel surfaces > show #8.2 models > hide #8.2 models > show #8.1 models > hide #!8 models > hide #8.1 models > hide #11.1 models > hide #!11 models > show #!8 models > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 139 hydrogen bonds found > show #8.1 models > show #8.2 models > hbonds #!8 reveal true 471 hydrogen bonds found > hide #11.2 models > select add #11 2314 atoms, 2371 bonds, 9 pseudobonds, 300 residues, 3 models selected > select subtract #11.1 1833 atoms, 1876 bonds, 7 pseudobonds, 242 residues, 4 models selected > select add #11 2314 atoms, 2371 bonds, 9 pseudobonds, 300 residues, 3 models selected > select subtract #11.2 481 atoms, 495 bonds, 2 pseudobonds, 58 residues, 4 models selected > select subtract #11.1 1 model selected > select add #8 2293 atoms, 2344 bonds, 284 pseudobonds, 300 residues, 3 models selected > select add #12 2293 atoms, 2344 bonds, 481 pseudobonds, 300 residues, 5 models selected > select add #13 2293 atoms, 2344 bonds, 610 pseudobonds, 300 residues, 5 models selected > hide #!8 models > hide #8.1 models > hide #8.2 models > select subtract #8 128 pseudobonds, 3 models selected > select add #8.1 1833 atoms, 128 pseudobonds, 242 residues, 2 models selected > select subtract #8.1 128 pseudobonds, 2 models selected > show #!11 models > select add #12 599 pseudobonds, 2 models selected > show #!8 models > hide #!11 models > show #12 models > show #13 models > select subtract #12 128 pseudobonds, 1 model selected > select add #13 139 pseudobonds, 1 model selected > select subtract #13 Nothing selected Drag select of 495 atoms, 238 residues, 415 bonds, 213 pseudobonds > select add #13 1814 atoms, 415 bonds, 343 pseudobonds, 240 residues, 5 models selected > select subtract #13 1814 atoms, 415 bonds, 204 pseudobonds, 240 residues, 4 models selected > select add #12 1814 atoms, 415 bonds, 471 pseudobonds, 240 residues, 4 models selected > select subtract #12 1814 atoms, 415 bonds, 240 residues, 3 models selected > select add #11 4128 atoms, 2786 bonds, 9 pseudobonds, 540 residues, 5 models selected > select subtract #11 1814 atoms, 415 bonds, 240 residues, 5 models selected Drag select of 271 atoms, 147 residues, 227 bonds, 132 pseudobonds > hide #!8 models > show #!8 models > select add #8 2293 atoms, 2344 bonds, 284 pseudobonds, 300 residues, 5 models selected > select subtract #8.1 460 atoms, 468 bonds, 58 pseudobonds, 58 residues, 5 models selected > select subtract #8.2 1 model selected Drag select of 275 atoms, 158 residues, 232 bonds, 133 pseudobonds > select subtract #8.1 1 model selected > ~hbonds > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 143 hydrogen bonds found > hbonds #!8 reveal true 464 hydrogen bonds found > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 143 hydrogen bonds found > hbonds /a:nad restrict cross log true reveal true Atom specifier selects no atoms > delete solvent > hide protein > hbonds sidechain restrict both reveal true color yellow radius .08 606 hydrogen bonds found > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 142 hydrogen bonds found Drag select of 221 atoms, 187 residues, 180 bonds, 33 pseudobonds > hide sel atoms > select subtract #8.1 1 model selected > color #8 #d6d6d6ff > color #8 silver > color #8 darkgrey > color #8 #d6d6d6ff > lighting simple > lighting soft > lighting full > lighting soft > graphics silhouettes true > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting flat > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting full > lighting soft > graphics silhouettes true Alignment identifier is 1.23/A Alignment identifier is 1 Alignment identifier is 3/A Alignment identifier is 4.20/A Alignment identifier is 2 Alignment identifier is 6/A Alignment identifier is 6/B Alignment identifier is 3 Alignment identifier is 4 Alignment identifier is 5 Alignment identifier is 8/A Alignment identifier is 6 Alignment identifier is 9/A Alignment identifier is 10/A Alignment identifier is 11/A > select #8/A:7-18,24-36,38-54 334 atoms, 337 bonds, 4 pseudobonds, 42 residues, 3 models selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:6-7 15 atoms, 14 bonds, 2 residues, 1 model selected > select #8/A:7-18,24-36,38-54 334 atoms, 337 bonds, 4 pseudobonds, 42 residues, 3 models selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:7-18,24-36,38-54 334 atoms, 337 bonds, 4 pseudobonds, 42 residues, 3 models selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:9 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:9-11 29 atoms, 29 bonds, 3 residues, 1 model selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:6-7 15 atoms, 14 bonds, 2 residues, 1 model selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:6-7 15 atoms, 14 bonds, 2 residues, 1 model selected > select #8/A:9 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:9-13 39 atoms, 39 bonds, 5 residues, 1 model selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:9 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:9-11 29 atoms, 29 bonds, 3 residues, 1 model selected > select #8/A:6,9-11 35 atoms, 34 bonds, 4 residues, 1 model selected > select #8/A:6,9-11,13-14 47 atoms, 45 bonds, 6 residues, 1 model selected > select #8/A:6,9-11,13-14,18 59 atoms, 57 bonds, 7 residues, 1 model selected > select #8/A:6,9-11,13-14,18,30 70 atoms, 68 bonds, 8 residues, 1 model selected > select #8/A:6,9-11,13-14,18,25,30 81 atoms, 79 bonds, 9 residues, 1 model selected > select #8/A:6,9-11,13-14,18,25,30 81 atoms, 79 bonds, 9 residues, 1 model selected > select #8/A:6,9-11,13-14,18,25,30,32 87 atoms, 84 bonds, 10 residues, 1 model selected > select #8/A:6,9-11,13-14,18,25,30,32 87 atoms, 84 bonds, 10 residues, 1 model selected > select #8/A:30 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/A:30-31 19 atoms, 19 bonds, 2 residues, 1 model selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > select #8/A:6,9-11 35 atoms, 34 bonds, 4 residues, 1 model selected > select #8/A:6,9-11,13-14 47 atoms, 45 bonds, 6 residues, 1 model selected > select #8/A:6,9-11,13-14,18 59 atoms, 57 bonds, 7 residues, 1 model selected > select #8/A:6,9-11,13-14,18,25 70 atoms, 68 bonds, 8 residues, 1 model selected > select #8/A:6,9-11,13-14,18,25,32 76 atoms, 73 bonds, 9 residues, 1 model selected > select #8/A:6,9-11,13-14,18,25,32,35 84 atoms, 80 bonds, 10 residues, 1 model selected > color (#!8 & sel) cornflower blue > show sel atoms > select #8/A:6,9-11,13-14,17-18,25,32,35 95 atoms, 91 bonds, 11 residues, 1 model selected > select #8/A:6,9-11,13-14,17-18,24-25,32,35 105 atoms, 102 bonds, 12 residues, 1 model selected > select #8/A:6,9-11,13-14,17-18,24-25,27-28,32,35 122 atoms, 118 bonds, 14 residues, 1 model selected > color (#!8 & sel) cornflower blue > select subtract #8.2 1 model selected > hide #!8 models > show #!9 models > hide #!9 surfaces Drag select of 269 atoms, 220 residues, 222 bonds, 28 pseudobonds > hide sel atoms > show sel atoms > select add #9 2297 atoms, 2349 bonds, 41 pseudobonds, 300 residues, 4 models selected > select subtract #9 2 models selected > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 145 hydrogen bonds found Drag select of 910 atoms, 221 residues, 768 bonds, 28 pseudobonds > select add #9 2297 atoms, 2349 bonds, 41 pseudobonds, 300 residues, 4 models selected > select subtract #9 2 models selected > select clear Drag select of 757 atoms, 188 residues, 636 bonds, 23 pseudobonds > hide sel atoms > color #9 #d6d6d6ff > select add #9 2297 atoms, 2349 bonds, 41 pseudobonds, 300 residues, 4 models selected > select subtract #9 2 models selected > select #9/A:6 10 atoms, 10 bonds, 1 residue, 1 model selected > select #9/A:6 10 atoms, 10 bonds, 1 residue, 1 model selected > select #9/A:6,9-11 36 atoms, 35 bonds, 4 residues, 1 model selected > select #9/A:6,9-11,13-14 52 atoms, 51 bonds, 6 residues, 1 model selected > select #9/A:6,9-11,13-14,17-18 77 atoms, 77 bonds, 8 residues, 1 model selected > select #9/A:6,9-11,13-14,17-18,24-25 95 atoms, 95 bonds, 10 residues, 1 model selected > select #9/A:6,9-11,13-14,17-18,24-25,27-28 112 atoms, 111 bonds, 12 residues, 1 model selected > select #9/A:6,9-11,13-14,17-18,24-25,27-28,32 119 atoms, 117 bonds, 13 residues, 1 model selected > select #9/A:6,9-11,13-14,17-18,24-25,27-28,32,35 126 atoms, 123 bonds, 14 residues, 1 model selected > color (#!9 & sel) cornflower blue > select add #9 2297 atoms, 2349 bonds, 41 pseudobonds, 300 residues, 4 models selected > select subtract #9 2 models selected > show #!8 models > tile 2 models tiled > lighting simple > select clear > hide #!8 models > hide #!9 models > show #!8 models > show #8.1 models > show #8.2 models > lighting soft > select #8/A:6,9-11,13-14,17-18,24-25,27-28,32,35 122 atoms, 118 bonds, 14 residues, 1 model selected > label (#!8 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > select subtract #8.2 1 model selected Drag select of 3 atoms, 2 residues, 4 bonds > select #8/A:4 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear Drag select of 3 atoms, 1 residues, 3 bonds > color (#!8 & sel) cornflower blue > label (#!8 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" > select subtract #8.2 1 model selected > hide #8.1 models > hide #8.2 models > hide #8.3 models > show #!9 models > matchmaker Missing or invalid ""matchAtoms"" argument: empty atom specifier > hide #!8 models > hide #!9 models > show #!11 models > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 142 hydrogen bonds found > color #11 #d6d6d6ff > lighting soft > lighting full > lighting soft > lighting simple > lighting soft Drag select of 263 atoms, 228 residues, 217 bonds, 31 pseudobonds > hide sel atoms > select add #11 2314 atoms, 2371 bonds, 44 pseudobonds, 300 residues, 4 models selected > select subtract #11 2 models selected > select #11/A:27 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!11 & sel) cornflower blue No visible atoms, bonds, or surfaces selected > select add #12 606 pseudobonds, 1 model selected > select subtract #12 Nothing selected > color #12 #fffb00ff models > undo > select #11/A:27 9 atoms, 8 bonds, 1 residue, 1 model selected > label (#!11 & sel) text ""{0.label_one_letter_code} > {0.number}{0.insertion_code}"" Drag select of 2 residues > select add #11 2314 atoms, 2371 bonds, 44 pseudobonds, 300 residues, 5 models selected > select subtract #11 2 models selected > show #!9 models > hide #!11 models > hide #!9 models > show #!9 models > select #9/A:6 10 atoms, 10 bonds, 1 residue, 1 model selected > select #9/A:10 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:6 10 atoms, 10 bonds, 1 residue, 1 model selected Drag select of 3 atoms, 2 residues, 3 bonds > select add #9/A:6 27 atoms, 13 bonds, 3 residues, 2 models selected > select #9/A:4 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/A:4-47 359 atoms, 367 bonds, 2 pseudobonds, 44 residues, 2 models selected > color (#!9 & sel) #d6d6d6ff > select add #12 359 atoms, 367 bonds, 606 pseudobonds, 44 residues, 3 models selected > select subtract #12 359 atoms, 367 bonds, 44 residues, 2 models selected > select subtract #9.1 1 model selected > select #9/A:9 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/A:9 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > select #9/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > select #9/A:7,17 20 atoms, 18 bonds, 2 residues, 1 model selected > select #9/A:9 9 atoms, 8 bonds, 1 residue, 1 model selected > select #9/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > select #9/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > select #9/A:9,17 20 atoms, 18 bonds, 2 residues, 1 model selected > color (#!9 & sel) cornflower blue > select subtract #9.1 1 model selected > hide #!9 models > show #!8 models > select #8/A:25 11 atoms, 11 bonds, 1 residue, 1 model selected > color (#!8 & sel) #c0c0c0ff > color (#!8 & sel) #d6d6d6ff > select #8/A:27 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!8 & sel) #c0c0c0ff > color (#!8 & sel) #d6d6d6ff > select #8/A:28 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > select clear > select #8/A:28 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!8 & sel) #c0c0c0ff > color (#!8 & sel) #d6d6d6ff > select #8/A:32 6 atoms, 5 bonds, 1 residue, 1 model selected > show sel atoms > color (#!8 & sel) #c0c0c0ff > color (#!8 & sel) #d6d6d6ff > select #8/A:35 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!8 & sel) #c0c0c0ff > color (#!8 & sel) #d6d6d6ff > select clear > select #8/A:18@CG 1 atom, 1 residue, 1 model selected > select #8/A:18 12 atoms, 12 bonds, 1 residue, 1 model selected > color (#!8 & sel) #c0c0c0ff > color (#!8 & sel) #d6d6d6ff > select #8/A:14 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:13 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/A:11 11 atoms, 10 bonds, 1 residue, 1 model selected Drag select of 5 atoms, 6 residues, 4 bonds > color (#!8 & sel) #c0c0c0ff > color (#!8 & sel) #d6d6d6ff > select subtract #8.2 1 model selected Drag select of 15 atoms, 7 residues, 12 bonds, 2 pseudobonds > select add #12 49 atoms, 12 bonds, 606 pseudobonds, 7 residues, 3 models selected > select subtract #12 49 atoms, 12 bonds, 7 residues, 2 models selected > select #8/A:6 6 atoms, 5 bonds, 1 residue, 1 model selected > color (#!8 & sel) #c0c0c0ff > color (#!8 & sel) #d6d6d6ff > show #!9 models > hide #!9 models > show #!9 models > hide #!9 models > show #!9 models > show #!11 models > hide #!8 models > select #11/A:21-22 16 atoms, 15 bonds, 2 residues, 1 model selected > select #11/A:21 8 atoms, 7 bonds, 1 residue, 1 model selected > select #11/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > select #11/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 138 hydrogen bonds found > hbonds sel reveal true 2 hydrogen bonds found > select add #11.2 1844 atoms, 10 bonds, 243 residues, 2 models selected > select subtract #11.1 1833 atoms, 242 residues, 3 models selected > select subtract #11.2 1 model selected > show #11.1 models > show #11.2 models > hide #!9 models > hide #9.1 models > hide #9.2 models > hide #!11 surfaces > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 141 hydrogen bonds found > hbonds #!11 reveal true 412 hydrogen bonds found > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 136 hydrogen bonds found > ~hbonds > hbonds #!11 reveal true 443 hydrogen bonds found > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 136 hydrogen bonds found Drag select of 427 atoms, 226 residues, 363 bonds, 186 pseudobonds > select subtract #11.2 1 model selected Drag select of 364 atoms, 206 residues, 305 bonds, 165 pseudobonds > hide sel atoms > undo > hide #12 models > show #12 models > hide #12 models > show #12 models > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 136 hydrogen bonds found > show #!10 models > hide #!10 models > show #!9 models > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 138 hydrogen bonds found > select add #12 443 pseudobonds, 1 model selected > select add #13 581 pseudobonds, 2 models selected > select subtract #12 138 pseudobonds, 1 model selected > select subtract #13 Nothing selected > select add #12 443 pseudobonds, 1 model selected > select subtract #12 Nothing selected > hide #11.1 models > hide #11.2 models > ~hbonds > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 138 hydrogen bonds found > hide #!9 models > hide #!11 models > show #!8 models > hbonds #!8 reveal true 407 hydrogen bonds found > show #!9 models > hide #!9 models > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 144 hydrogen bonds found > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 145 hydrogen bonds found > hide #12 models > show #12 models > ~hbonds > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 142 hydrogen bonds found > hbonds #!8 reveal true 389 hydrogen bonds found > interModel true Unknown command: interModel true > interfaces #!8 & ~solvent 1 buried areas: B A 910 > tile off > hbonds #!8 reveal true 423 hydrogen bonds found Drag select of 797 atoms, 300 residues, 669 bonds, 284 pseudobonds > hide sel atoms > close #12 > select add #13 2293 atoms, 669 bonds, 142 pseudobonds, 300 residues, 4 models selected > select subtract #13 2293 atoms, 669 bonds, 300 residues, 3 models selected > close #13 > hide #11.3 models > show #11.3 models > select add #8 2293 atoms, 2344 bonds, 300 residues, 4 models selected > select subtract #8 2 models selected > hide #!11 models > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 142 hydrogen bonds found > hbonds #!8 reveal true 423 hydrogen bonds found > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 142 hydrogen bonds found > hbonds /a:nad restrict cross log true reveal true Atom specifier selects no atoms > delete solvent > hide protein > hbonds sidechain restrict both reveal true color yellow radius .08 531 hydrogen bonds found > hbonds sidechain restrict both saltOnly true name ""salt bridges"" color > magenta radius .1 142 hydrogen bonds found Drag select of 3 atoms, 4 residues, 1 pseudobonds > select clear > show #!9 models > show #!11 models > tile 3 models tiled > hide #12 models > show #12 models > hide #13 models > show #13 models Drag select of 6 pseudobonds > select clear Drag select of 43 atoms, 29 residues, 36 bonds, 4 pseudobonds Drag select of 32 atoms, 26 residues, 24 bonds, 8 pseudobonds > select add #12 207 atoms, 24 bonds, 148 pseudobonds, 31 residues, 5 models selected > select subtract #12 207 atoms, 24 bonds, 6 pseudobonds, 31 residues, 4 models selected > select add #13 207 atoms, 24 bonds, 531 pseudobonds, 31 residues, 4 models selected > select subtract #13 207 atoms, 24 bonds, 31 residues, 3 models selected > select subtract #8.2 15 atoms, 4 bonds, 5 residues, 3 models selected > select subtract #8.1 1 model selected Drag select of 5 pseudobonds > select clear Drag select of 5 pseudobonds Drag select of 25 atoms, 19 residues, 21 bonds, 7 pseudobonds > select clear Drag select of 1 atoms, 5 pseudobonds > hide (#!8 & sel) target a > delete atoms (#!8 & sel) > delete bonds (#!8 & sel) > hide #!11 models > lighting soft > hide #!9 models > hide #!8 models > show #!9 models > hide #!9 models > show #!11 models > show #!9 models > show #!8 models > hide #!11 models > lighting soft > hide #!9 models > ui mousemode right rotate > ui mousemode right translate > ui mousemode right rotate > ui mousemode right translate > undo Drag select of 23 atoms, 16 residues, 19 bonds, 1 pseudobonds > select subtract #8.1 1 model selected > show #!9 models > select #8/A:24 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/A:24 10 atoms, 10 bonds, 1 residue, 1 model selected > color (#!8 & sel) #941100ff > select #8/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!8 & sel) #ff2600ff > color (#!8 & sel) #941100ff > select #8/A:9 10 atoms, 10 bonds, 1 residue, 1 model selected > color (#!8 & sel) #ff2600ff > color (#!8 & sel) #941100ff > select clear > select #8/A:10 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!8 & sel) #945200ff > color (#!8 & sel) #941100ff > select #8/A:3 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!8 & sel) #945200ff > color (#!8 & sel) #941100ff > select #8/B:165 7 atoms, 6 bonds, 1 residue, 1 model selected > color (#!8 & sel) #0433ffff > color (#!8 & sel) #0096ffff > color (#!8 & sel) #0433ffff > color (#!8 & sel) #0433ff7f > select #8/B:226@CG 1 atom, 1 residue, 1 model selected > select #8/B:184 12 atoms, 12 bonds, 1 residue, 1 model selected > color (#!8 & sel) #0433ffff > color (#!8 & sel) #0433ff80 > select #8/B:103 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!8 & sel) #0433ffff > color (#!8 & sel) #0433ff7e > color (#!8 & sel) #0433ff7d > select #8/B:102 12 atoms, 12 bonds, 1 residue, 1 model selected > color (#!8 & sel) #0433ffff > color (#!8 & sel) #0433ff7d > select clear > select #8/B:53 6 atoms, 5 bonds, 1 residue, 1 model selected > color (#!8 & sel) #0433ffff > color (#!8 & sel) #0433ff7c > select #8/B:73 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!8 & sel) #0433ffff > color (#!8 & sel) #0433ff81 > hide #!9 models > show #!9 models > select #9/A:9 9 atoms, 8 bonds, 1 residue, 1 model selected > ui tool show ""Color Actions"" > color (#!9 & sel) #941100ff > select #9/A:17 11 atoms, 10 bonds, 1 residue, 1 model selected > color (#!9 & sel) #ff2600ff > color (#!9 & sel) #941100ff > select #9/B:53 6 atoms, 5 bonds, 1 residue, 1 model selected > color (#!9 & sel) #0433ffff > color (#!9 & sel) #0433ff80 > color (#!9 & sel) #0433ff7f > select #9/B:184 12 atoms, 12 bonds, 1 residue, 1 model selected > color (#!9 & sel) #0433ffff > color (#!9 & sel) #0433ff79 > show #!11 models > hide #!8 models > select #11/A:27 9 atoms, 8 bonds, 1 residue, 1 model selected > color (#!11 & sel) #941100ff > select #11/B:227 8 atoms, 7 bonds, 1 residue, 1 model selected > select #11/B:226 8 atoms, 7 bonds, 1 residue, 1 model selected > select #11/B:227 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!11 & sel) #0433ffff > color (#!11 & sel) #0433ff7e > select #11/B:226 8 atoms, 7 bonds, 1 residue, 1 model selected > color (#!11 & sel) #0433ffff > color (#!11 & sel) #0433ff82 Drag select of 212 atoms, 214 residues, 180 bonds, 28 pseudobonds > hide sel atoms > show #!8 models Drag select of 181 atoms, 173 residues, 150 bonds, 30 pseudobonds > hide sel atoms Drag select of 24 atoms, 49 residues, 19 bonds > hide sel atoms Drag select of 2 atoms, 2 residues, 2 bonds > hide sel atoms Drag select of 3 atoms, 2 residues, 2 bonds > hide sel atoms Drag select of 3 atoms, 2 residues, 6 bonds > hide sel atoms Drag select of 3 atoms, 163 residues, 4 bonds > hide sel atoms > select clear Drag select of 10 atoms, 6 bonds, 1 pseudobonds > hide sel atoms Drag select of 25 atoms, 60 residues, 17 bonds, 4 pseudobonds Drag select of 5 residues Drag select of 4 atoms, 69 residues, 2 bonds > hide sel atoms Drag select of 1 atoms, 1 residues, 1 bonds Drag select of 2 atoms, 4 residues, 1 bonds > hide sel atoms Drag select of 14 residues > select add #8 2292 atoms, 2343 bonds, 57 pseudobonds, 300 residues, 5 models selected > select subtract #8 2 models selected Drag select of 23 atoms, 234 residues, 23 bonds Drag select of 204 residues > hide sel atoms Drag select of 8 atoms, 17 residues, 6 bonds > hide sel atoms Drag select of 17 atoms, 60 residues, 16 bonds > hide sel atoms Drag select of 137 atoms, 175 residues, 115 bonds, 23 pseudobonds > hide sel atoms Drag select of 11 atoms, 63 residues, 7 bonds, 1 pseudobonds > hide sel atoms Drag select of 32 atoms, 50 residues, 27 bonds, 3 pseudobonds Drag select of 3 residues Drag select of 15 atoms, 67 residues, 13 bonds, 1 pseudobonds > hide sel atoms Drag select of 4 atoms, 28 residues, 3 bonds > hide sel atoms Drag select of 6 atoms, 42 residues, 5 bonds > hide sel atoms Drag select of 4 atoms, 58 residues, 3 bonds > hide sel atoms ===== Log before crash end ===== Log: 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 OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M3 Pro OpenGL vendor: Apple 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: Mac15,6 Model Number: MRX43KS/A Chip: Apple M3 Pro Total Number of Cores: 12 (6 performance and 6 efficiency) Memory: 18 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 12 days, 17 hours, 32 minutes Graphics/Displays: Apple M3 Pro: Chipset Model: Apple M3 Pro Type: GPU Bus: Built-In Total Number of Cores: 18 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported 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 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 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 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 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 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 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 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 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