id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19006 Crash on Mac waking from sleep gotla.suhas@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.6.1-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. suhas's comments: I stepped away from my laptop for a few mins and it went to sleep, and chimeraX crashed when i reopened my laptop. Fatal Python error: Segmentation fault Current thread 0x00000001f8dda0c0 (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.pdb_lib._load_libs, chimerax.surface._surface, 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.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2025-10-01 13:35:37.00 -0400"",""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 15.6.1 (24G90)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""57CA26B5-9683-4A8D-8F08-87A4DFDF2AA6""} { ""uptime"" : 550000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""Mac15,12"", ""coalitionID"" : 22551, ""osVersion"" : { ""train"" : ""macOS 15.6.1"", ""build"" : ""24G90"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-10-01 13:35:31.4869 -0400"", ""codeSigningMonitor"" : 1, ""incident"" : ""57CA26B5-9683-4A8D-8F08-87A4DFDF2AA6"", ""pid"" : 85153, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-09-30 09:08:23.5320 -0400"", ""procStartAbsTime"" : 12330364558369, ""procExitAbsTime"" : 13278368640360, ""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"":""CFDC5ADD-BD23-54F7-ABE9-67DF663965BE"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""9F9E57F5-547E-D476-8C06-E64738D3D883"", ""appleIntelligenceStatus"" : {""state"":""unavailable"",""reasons"":[""siriAssetIsNotReady"",""assetIsNotReady"",""notOptedIn""]}, ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""codeSigningAuxiliaryInfo"" : 0, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRm+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkZDg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""01F4A0AE-C30B-46F6-A555-EB915012A58F"", ""sleepWakeUUID"" : ""D38D4C54-142E-48CC-A947-1DE863EAF5ED"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x141b7ba83448 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > set bgColor white > cd > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates Current working directory is: /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates > open > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/pdb_templates/9ut9_tas1r2_only.pdb Chain information for 9ut9_tas1r2_only.pdb #1 --- Chain | Description A | No description available > open > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/v1/boltz_results_v1/predictions/v1/v1_model_0.cif Summary of feedback from opening /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/v1/boltz_results_v1/predictions/v1/v1_model_0.cif --- warning | Unable to fetch template for 'LIG1': will connect using distance criteria v1_model_0.cif title: . [more info...] Chain information for v1_model_0.cif #2 --- Chain | Description A | . Non-standard residues in v1_model_0.cif #2 --- LIG1 — (LIG1) No chain in structure corresponds to chain ID given in local score info (chain 'B') > close #1 > open > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/pdb_templates/9utc_tas1r2_sucralose_only.pdb Summary of feedback from opening /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/pdb_templates/9utc_tas1r2_sucralose_only.pdb --- warnings | Start residue of secondary structure not found: HELIX 16 16 SER B 26 ARG B 30 1 5 Start residue of secondary structure not found: HELIX 17 17 SER B 66 LYS B 86 1 21 Start residue of secondary structure not found: HELIX 18 18 PRO B 106 PHE B 116 1 11 Start residue of secondary structure not found: HELIX 19 19 SER B 146 LEU B 161 1 16 Start residue of secondary structure not found: HELIX 20 20 SER B 189 PHE B 204 1 16 28 messages similar to the above omitted Cannot find LINK/SSBOND residue CYS (24 ) Cannot find LINK/SSBOND residue CYS (62 ) Cannot find LINK/SSBOND residue CYS (236 ) Cannot find LINK/SSBOND residue CYS (370 ) Cannot find LINK/SSBOND residue CYS (410 ) 4 messages similar to the above omitted 9utc_tas1r2_sucralose_only.pdb title: The VFT domains of human sweet taste receptor TAS1R2 and TAS1R3 In the sucralose-bound state [more info...] Chain information for 9utc_tas1r2_sucralose_only.pdb #1 --- Chain | Description | UniProt A | taste receptor type 1 member 2,taste receptor type 1 member 2,engineered red fluorescent protein MSCARLET3 | TS1R2_HUMAN 26-839 Non-standard residues in 9utc_tas1r2_sucralose_only.pdb #1 --- RRJ — 4-chloro-4-deoxy-α-D-galactopyranose RRY — 1,6-dichloro-1,6-dideoxy-β-D-fructofuranose > open > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/v2/boltz_results_v2/predictions/v2/v2_model_0.cif Summary of feedback from opening /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/v2/boltz_results_v2/predictions/v2/v2_model_0.cif --- warning | Unable to fetch template for 'LIG1': will connect using distance criteria v2_model_0.cif title: . [more info...] Chain information for v2_model_0.cif #3 --- Chain | Description A | . Non-standard residues in v2_model_0.cif #3 --- LIG1 — (LIG1) No chain in structure corresponds to chain ID given in local score info (chain 'B') > mmaker #2 to #1 showAlignment t 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 9utc_tas1r2_sucralose_only.pdb, chain A (#1) with v1_model_0.cif, chain A (#2), sequence alignment score = 2525.9 Alignment identifier is 1 Showing conservation header (""seq_conservation"" residue attribute) for alignment 1 Hiding conservation header for alignment 1 Chains used in RMSD evaluation for alignment 1: 9utc_tas1r2_sucralose_only.pdb #1/A, v1_model_0.cif #2/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 1 RMSD between 457 pruned atom pairs is 0.980 angstroms; (across all 500 pairs: 1.282) > mmaker #3 to #1 showAlignment t 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 9utc_tas1r2_sucralose_only.pdb, chain A (#1) with v2_model_0.cif, chain A (#3), sequence alignment score = 2510.6 Alignment identifier is 2 Showing conservation header (""seq_conservation"" residue attribute) for alignment 2 Hiding conservation header for alignment 2 Chains used in RMSD evaluation for alignment 2: 9utc_tas1r2_sucralose_only.pdb #1/A, v2_model_0.cif #3/A Showing rmsd header (""seq_rmsd"" residue attribute) for alignment 2 RMSD between 398 pruned atom pairs is 1.043 angstroms; (across all 500 pairs: 1.769) > hide #3 models > view > save > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/results_representations.cxs > rename #2 3_no_template_wt_aka_v1_model_0.cif > rename #3 3_no_template_y103_aka_v2v2_model_0.cif > rename #3 3_no_template_y103_aka_v2_model_0.cif > mmaker #2 ro #1 > matchmaker #2 ro #1 Expected a keyword > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc_tas1r2_sucralose_only.pdb, chain A (#1) with 3_no_template_wt_aka_v1_model_0.cif, chain A (#2), sequence alignment score = 2525.9 RMSD between 457 pruned atom pairs is 0.980 angstroms; (across all 500 pairs: 1.282) > renumber #2/A seqStart 26 527 residues renumbered > rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,103,142,143,165,277,278,302,303,306 RMSD between 103 atom pairs is 1.405 > save > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/3_no_templates/results_representations.cxs > open > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/2_apo_templates/results_visualization.cxs opened ChimeraX session > rename #3 2_apo_y103a_aka_v2_model_0.cif > show #!1 models > hide #3 models > hide #2 models > mmaker #2 ro #1 > matchmaker #2 ro #1 Expected a keyword > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 2_apo_wt_v1_model_0.cif, chain A (#2), sequence alignment score = 2525.3 RMSD between 447 pruned atom pairs is 0.979 angstroms; (across all 500 pairs: 1.367) > renumber #2/A seqStart 26 0 residues renumbered > show #2 models > rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,103,142,143,165,277,278,302,303,306 RMSD between 103 atom pairs is 1.356 > select :40,65,67,71,103,142,143,165,277,278,302,303,306 302 atoms, 277 bonds, 39 residues, 3 models selected > show sel > label sel > view sel > hide ~sel > select ~sel 12274 atoms, 12570 bonds, 2 pseudobonds, 1519 residues, 7 models selected > hide sel > show sel & #!1-2 cartoons > hide sel & #!1-2 cartoons > select ligand 69 atoms, 72 bonds, 4 residues, 3 models selected > show sel & #!1-2 atoms > open > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/results_visualization.cxs opened ChimeraX session > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 1_holo_wt_aka_v2_model_0.cif, chain A (#2), sequence alignment score = 2512.1 RMSD between 431 pruned atom pairs is 0.935 angstroms; (across all 500 pairs: 1.638) > renumber #2/A seqStart 26 527 residues renumbered > rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #3:40,65,67,71,103,142,143,165,277,278,302,303,306 Number of atoms from first atom spec (103) differs from number in second (96) > rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #3:40,65,67,71,103,142,143,165,277,278,302,303,306 Number of atoms from first atom spec (103) differs from number in second (96) > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 1_holo_wt_aka_v2_model_0.cif, chain A (#2), sequence alignment score = 2512.1 RMSD between 431 pruned atom pairs is 0.935 angstroms; (across all 500 pairs: 1.638) > renumber #2/A seqStart 26 0 residues renumbered > rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,103,142,143,165,277,278,302,303,306 Number of atoms from first atom spec (103) differs from number in second (203) > rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,103,142,143,165,277,278,302,303,306 Number of atoms from first atom spec (103) differs from number in second (203) > rmsd #1:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #2:40,65,67,71,103,142,143,165,277,278,302,303,306 Number of atoms from first atom spec (203) differs from number in second (103) > rmsd #1/A:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #2:40,65,67,71,103,142,143,165,277,278,302,303,306 RMSD between 103 atom pairs is 1.322 > select #1/B 4084 atoms, 4192 bonds, 1 pseudobond, 526 residues, 2 models selected > delete sel > select ligand 69 atoms, 72 bonds, 4 residues, 3 models selected > view sel > select all 12576 atoms, 12907 bonds, 2 pseudobonds, 1558 residues, 5 models selected > hide sel & #!1,3 cartoons > hide #!3 models > show #2 models > hide sel & #2#!1 cartoons > select subtract #3 8321 atoms, 8542 bonds, 2 pseudobonds, 1030 residues, 3 models selected > select all 12576 atoms, 12907 bonds, 2 pseudobonds, 1558 residues, 5 models selected > hide sel & #2#!1 cartoons > hide sel & #2#!1 atoms > select ligand 69 atoms, 72 bonds, 4 residues, 3 models selected > show sel & #2#!1 atoms > select add #3 4301 atoms, 4413 bonds, 531 residues, 4 models selected > select subtract #3 46 atoms, 48 bonds, 3 residues, 2 models selected > select all 12576 atoms, 12907 bonds, 2 pseudobonds, 1558 residues, 5 models selected > show sel & #2#!1 cartoons > select :103 29 atoms, 28 bonds, 3 residues, 3 models selected > show sel & #2#!1 atoms > view > hide #2 models > select zone ligand 4 protein residues true Selected 447 atoms > show sel & #!1 atoms > show #2 models > hide #!1 models > select ligand 69 atoms, 72 bonds, 4 residues, 3 models selected > view > view sel > show hydrogen Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show ligand > show #!1 models > select protein 12507 atoms, 12835 bonds, 2 pseudobonds, 1554 residues, 4 models selected > hide sel & #2#!1 cartoons > select ligand,:103 Expected an objects specifier or a keyword > select :103,LIG1,rryrrj 75 atoms, 76 bonds, 5 residues, 3 models selected > select :103,LIG1,rry,rrj 98 atoms, 100 bonds, 7 residues, 3 models selected > select ~sel 12478 atoms, 12801 bonds, 2 pseudobonds, 1551 residues, 5 models selected > hide sel & #2#!1 atoms > hide #2 models > select zone 4 ligand protein res t Missing or invalid ""near"" argument: invalid objects specifier > select zone ligand 4 protein residues true Selected 447 atoms > select #1 & (zone ligand 4 protein res t) Expected a keyword > select (zone #1 & ligand 4 #1 & protein res t) Expected an objects specifier or a keyword > select (zone #1 & ligand 4 (#1 & protein) res t) Expected an objects specifier or a keyword > select zone #1 & ligand 4 (#1 & protein) residues true Selected 103 atoms > show sel atoms > view sel > label sel > view sel > select sel & @CA 13 atoms, 13 residues, 1 model selected > select ~sel & !:rry,rrj Expected a keyword > select ~sel &! :rry,rrj Expected a keyword > select ~sel 12563 atoms, 12868 bonds, 2 pseudobonds, 1558 residues, 6 models selected > hide sel & #!1 atoms > undo > select clear > select :rrj,rry 23 atoms, 24 bonds, 2 residues, 1 model selected > style sel sphere Changed 23 atom styles > style sel ball Changed 23 atom styles > hide sel atoms > show sel atoms > select up 4059 atoms, 4169 bonds, 502 residues, 1 model selected > select up 12576 atoms, 12907 bonds, 1558 residues, 3 models selected > select up 12576 atoms, 12907 bonds, 1558 residues, 3 models selected > select down 4059 atoms, 4169 bonds, 502 residues, 1 model selected > select down 23 atoms, 24 bonds, 2 residues, 1 model selected > select down 23 atoms, 24 bonds, 2 residues, 1 model selected > select down 23 atoms, 24 bonds, 2 residues, 1 model selected Drag select of 126 atoms, 119 bonds > info selection atom id #1/A:40@N idatm_type Npl atom id #1/A:40@CA idatm_type C3 atom id #1/A:40@C idatm_type C2 atom id #1/A:40@O idatm_type O2 atom id #1/A:40@CB idatm_type C3 atom id #1/A:40@OG idatm_type O3 atom id #1/A:65@N idatm_type Npl atom id #1/A:65@CA idatm_type C3 atom id #1/A:65@C idatm_type C2 atom id #1/A:65@O idatm_type O2 atom id #1/A:65@CB idatm_type C3 atom id #1/A:65@CG idatm_type C3 atom id #1/A:65@CD idatm_type C3 atom id #1/A:65@CE idatm_type C3 atom id #1/A:65@NZ idatm_type N3+ atom id #1/A:67@N idatm_type Npl atom id #1/A:67@CA idatm_type C3 atom id #1/A:67@C idatm_type C2 atom id #1/A:67@O idatm_type O2 atom id #1/A:67@CB idatm_type C3 atom id #1/A:67@CG1 idatm_type C3 atom id #1/A:67@CG2 idatm_type C3 atom id #1/A:67@CD1 idatm_type C3 atom id #1/A:71@N idatm_type Npl atom id #1/A:71@CA idatm_type C3 atom id #1/A:71@C idatm_type C2 atom id #1/A:71@O idatm_type O2 atom id #1/A:71@CB idatm_type C3 atom id #1/A:71@CG idatm_type C3 atom id #1/A:71@CD1 idatm_type C3 atom id #1/A:71@CD2 idatm_type C3 atom id #1/A:103@N idatm_type Npl atom id #1/A:103@CA idatm_type C3 atom id #1/A:103@C idatm_type C2 atom id #1/A:103@O idatm_type O2 atom id #1/A:103@CB idatm_type C3 atom id #1/A:103@CG idatm_type Car atom id #1/A:103@CD1 idatm_type Car atom id #1/A:103@CD2 idatm_type Car atom id #1/A:103@CE1 idatm_type Car atom id #1/A:103@CE2 idatm_type Car atom id #1/A:103@CZ idatm_type Car atom id #1/A:103@OH idatm_type O3 atom id #1/A:142@N idatm_type Npl atom id #1/A:142@CA idatm_type C3 atom id #1/A:142@C idatm_type C2 atom id #1/A:142@O idatm_type O2 atom id #1/A:142@CB idatm_type C3 atom id #1/A:142@CG idatm_type Cac atom id #1/A:142@OD1 idatm_type O2- atom id #1/A:142@OD2 idatm_type O2- atom id #1/A:143@N idatm_type Npl atom id #1/A:143@CA idatm_type C3 atom id #1/A:143@C idatm_type C2 atom id #1/A:143@O idatm_type O2 atom id #1/A:143@CB idatm_type C3 atom id #1/A:143@CG idatm_type C2 atom id #1/A:143@OD1 idatm_type O2 atom id #1/A:143@ND2 idatm_type Npl atom id #1/A:165@N idatm_type Npl atom id #1/A:165@CA idatm_type C3 atom id #1/A:165@C idatm_type C2 atom id #1/A:165@O idatm_type O2 atom id #1/A:165@CB idatm_type C3 atom id #1/A:165@OG idatm_type O3 atom id #1/A:277@N idatm_type Npl atom id #1/A:277@CA idatm_type C3 atom id #1/A:277@C idatm_type C2 atom id #1/A:277@O idatm_type O2 atom id #1/A:277@CB idatm_type C3 atom id #1/A:277@CG idatm_type C3 atom id #1/A:277@CD idatm_type C3 atom id #1/A:278@N idatm_type Npl atom id #1/A:278@CA idatm_type C3 atom id #1/A:278@C idatm_type C2 atom id #1/A:278@O idatm_type O2 atom id #1/A:278@CB idatm_type C3 atom id #1/A:278@CG idatm_type Cac atom id #1/A:278@OD1 idatm_type O2- atom id #1/A:278@OD2 idatm_type O2- atom id #1/A:302@N idatm_type Npl atom id #1/A:302@CA idatm_type C3 atom id #1/A:302@C idatm_type C2 atom id #1/A:302@O idatm_type O2 atom id #1/A:302@CB idatm_type C3 atom id #1/A:302@CG idatm_type C3 atom id #1/A:302@CD idatm_type Cac atom id #1/A:302@OE1 idatm_type O2- atom id #1/A:302@OE2 idatm_type O2- atom id #1/A:303@N idatm_type Npl atom id #1/A:303@CA idatm_type C3 atom id #1/A:303@C idatm_type C2 atom id #1/A:303@O idatm_type O2 atom id #1/A:303@CB idatm_type C3 atom id #1/A:303@OG idatm_type O3 atom id #1/A:306@N idatm_type Npl atom id #1/A:306@CA idatm_type C3 atom id #1/A:306@C idatm_type C2 atom id #1/A:306@O idatm_type O2 atom id #1/A:306@CB idatm_type C3 atom id #1/A:306@CG1 idatm_type C3 atom id #1/A:306@CG2 idatm_type C3 atom id #1/A:306@CD1 idatm_type C3 atom id #1/C:1@O3 idatm_type O3 atom id #1/C:1@C3 idatm_type C3 atom id #1/C:1@C4 idatm_type C3 atom id #1/C:1@O4 idatm_type O3 atom id #1/C:1@C5 idatm_type C3 atom id #1/C:1@C6 idatm_type C3 atom id #1/C:1@CL6 idatm_type Cl atom id #1/C:1@O5 idatm_type O3 atom id #1/C:1@C2 idatm_type C3 atom id #1/C:1@C1 idatm_type C3 atom id #1/C:1@CL1 idatm_type Cl atom id #1/C:1@O2 idatm_type O3 atom id #1/C:2@C1 idatm_type C3 atom id #1/C:2@O5 idatm_type O3 atom id #1/C:2@C5 idatm_type C3 atom id #1/C:2@C6 idatm_type C3 atom id #1/C:2@O6 idatm_type O3 atom id #1/C:2@C4 idatm_type C3 atom id #1/C:2@CL4 idatm_type Cl atom id #1/C:2@C3 idatm_type C3 atom id #1/C:2@O3 idatm_type O3 atom id #1/C:2@C2 idatm_type C3 atom id #1/C:2@O2 idatm_type O3 > info residues sel residue id #1/A:40 name SER index 43 residue id #1/A:65 name LYS index 68 residue id #1/A:67 name ILE index 70 residue id #1/A:71 name LEU index 74 residue id #1/A:103 name TYR index 106 residue id #1/A:142 name ASP index 145 residue id #1/A:143 name ASN index 146 residue id #1/A:165 name SER index 168 residue id #1/A:277 name PRO index 280 residue id #1/A:278 name ASP index 281 residue id #1/A:302 name GLU index 305 residue id #1/A:303 name SER index 306 residue id #1/A:306 name ILE index 309 residue id #1/C:1 name RRY residue id #1/C:2 name RRJ Drag select of 126 atoms, 119 bonds > ui tool show ""Side View"" > movie record > turn y 2 180 > wait 180 > movie encode /Users/suhasgotla/Desktop/movie1.mp4 Movie saved to /Users/suhasgotla/Desktop/movie1.mp4 > view > hide #!1 models > show #!3 models > hide #!3 models > show #2 models > select add #1 4059 atoms, 4169 bonds, 2 pseudobonds, 502 residues, 3 models selected > select add #2 8321 atoms, 8542 bonds, 2 pseudobonds, 1030 residues, 4 models selected > select subtract #1 4262 atoms, 4373 bonds, 528 residues, 1 model selected Drag select of 23 atoms, 24 bonds > label sel > info selection atom id #2/B:1@O23 idatm_type O3 atom id #2/B:1@C32 idatm_type C3 atom id #2/B:1@C41 idatm_type C3 atom id #2/B:1@O29 idatm_type O3 atom id #2/B:1@C34 idatm_type C3 atom id #2/B:1@O24 idatm_type O3 atom id #2/B:1@C35 idatm_type C3 atom id #2/B:1@C31 idatm_type C3 atom id #2/B:1@CL20 idatm_type Cl atom id #2/B:1@O30 idatm_type O3 atom id #2/B:1@C42 idatm_type C3 atom id #2/B:1@C33 idatm_type C3 atom id #2/B:1@CL21 idatm_type Cl atom id #2/B:1@C39 idatm_type C3 atom id #2/B:1@O27 idatm_type O3 atom id #2/B:1@C40 idatm_type C3 atom id #2/B:1@O28 idatm_type O3 atom id #2/B:1@C37 idatm_type C3 atom id #2/B:1@O25 idatm_type O3 atom id #2/B:1@C38 idatm_type C3 atom id #2/B:1@O26 idatm_type O3 atom id #2/B:1@C36 idatm_type C3 atom id #2/B:1@CL22 idatm_type Cl > select #2/B:1@CL22 1 atom, 1 residue, 1 model selected > label sel > selete label Unknown command: selete label > delete label Missing or invalid ""atoms"" argument: invalid atoms specifier > label delete Drag select of 11 atoms, 12 bonds Drag select of 12 atoms, 12 bonds > hide sel atoms Drag select of 23 atoms, 24 bonds > label sel atoms > save /Users/suhasgotla/Desktop/image1.png supersample 3 > save /Users/suhasgotla/Desktop/image2.png supersample 3 > hide #!2 models > select add #2 4262 atoms, 4373 bonds, 528 residues, 2 models selected > show #!1 models > select subtract #2 Nothing selected > ui tool show Distances Exactly two atoms must be selected! > select #1/A:142@CG 1 atom, 1 residue, 1 model selected > select add #1/C:2@O5 2 atoms, 2 residues, 1 model selected > distance #1/A:142@CG #1/C:2@O5 Distance between 9utc.pdb #1/A ASP 142 CG and /C RRJ 2 O5: 3.060Å > view sel > ui tool show ""Side View"" > label sel atoms > label sel residues Drag select of 13 atoms, 12 bonds > hide sel atoms Drag select of 6 atoms, 5 bonds > hide sel atoms Drag select of 3 atoms, 2 bonds Drag select of 11 atoms, 10 bonds > hide sel atoms Drag select of 7 atoms, 2 bonds > hide sel atoms Drag select of 6 atoms, 3 bonds > hide sel atoms Drag select of 6 atoms, 5 bonds > hide sel atoms Drag select of 8 atoms, 7 bonds > hide sel atoms Drag select of 6 atoms, 5 bonds > hide sel atoms Drag select of 9 atoms, 8 bonds > hide sel atoms Drag select of 7 atoms, 6 bonds > hide sel atoms Drag select of 8 atoms, 8 bonds > hide sel atoms > view > save /Users/suhasgotla/Desktop/image1.png supersample 3 > show #!2 models > hide #!1 models > show #2/142 > show #2:142 > select #2/A:142@CG 1 atom, 1 residue, 1 model selected > select #2/B:1@O29 1 atom, 1 residue, 1 model selected > select add #2/A:142@CG 2 atoms, 2 residues, 1 model selected > distance #2/B:1@O29 #2/A:142@CG Distance between 1_holo_wt_aka_v2_model_0.cif #2/B LIG1 1 O29 and /A ASP 142 CG: 7.365Å > hide #!2 models > show #!1 models > select add #1 4061 atoms, 4169 bonds, 3 pseudobonds, 504 residues, 5 models selected > show #!2 models > hide #!1 models > label delete ~sel > select #2/A:142@CG 1 atom, 1 residue, 1 model selected > label atoms sel Expected a keyword > label sel atoms > label sel residues > select add #2/B:1@O29 1 atom, 1 pseudobond, 1 residue, 2 models selected > select add #2/A:142@CG 2 atoms, 1 pseudobond, 2 residues, 2 models selected > view sel > save /Users/suhasgotla/Desktop/image1.png supersample 3 > hide #!2 models > select add #2 4262 atoms, 4373 bonds, 1 pseudobond, 528 residues, 3 models selected > show #3 models > select subtract #2 Nothing selected > select add #3 4255 atoms, 4365 bonds, 528 residues, 1 model selected > select #3,ligand Expected an objects specifier or a keyword > select #3&ligand 23 atoms, 24 bonds, 1 residue, 1 model selected > select #3/A:302@CA 1 atom, 1 residue, 1 model selected > select add #3/A:302@CB 2 atoms, 1 residue, 1 model selected > select #3&ligand 23 atoms, 24 bonds, 1 residue, 1 model selected > select add #3:142 31 atoms, 31 bonds, 2 residues, 1 model selected > hide ~sel > select #3/A:142@CG 1 atom, 1 residue, 1 model selected > select add #3/B:1@O29 2 atoms, 2 residues, 1 model selected > label sel atoms > label :142 > select #3/A:142@CG 1 atom, 1 residue, 1 model selected > select add #3/B:1@O29 2 atoms, 2 residues, 1 model selected > distance #3/A:142@CG #3/B:1@O29 Distance between 1_holo_y103a_aka_v3_model_0.cif #3/A ASP 142 CG and /B LIG1 1 O29: 6.600Å > save /Users/suhasgotla/Desktop/image1.png supersample 3 > open > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/v4/boltz_results_v4/predictions/v4/v4_model_0.cif Summary of feedback from opening /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/v4/boltz_results_v4/predictions/v4/v4_model_0.cif --- warning | Unable to fetch template for 'LIG1': will connect using distance criteria v4_model_0.cif title: . [more info...] Chain information for v4_model_0.cif #5 --- Chain | Description A | . Non-standard residues in v4_model_0.cif #5 --- LIG1 — (LIG1) No chain in structure corresponds to chain ID given in local score info (chain 'B') > rename #5 1_holo_wt_pocket_aka_v4_model_0.cif > hide #5 models > show #5 models > hide #4.1 models > hide #!4 models > hide #!3 models > view > show #!1 models > view > clear Unknown command: clear > clear Unknown command: clear > mmaker #4 to #1 No molecules/chains to match specified > mmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 1_holo_wt_pocket_aka_v4_model_0.cif, chain A (#5), sequence alignment score = 2531.9 RMSD between 431 pruned atom pairs is 0.958 angstroms; (across all 500 pairs: 1.520) > select add #1 4061 atoms, 4169 bonds, 3 pseudobonds, 504 residues, 5 models selected > show sel & #!1 cartoons > select subtract #1 2 atoms, 2 residues, 1 model selected > view > show #1&ligand > view sel No displayed objects specified. > select ligand 92 atoms, 96 bonds, 5 residues, 4 models selected > view sel > hide #!1 models > select #5&ligand 23 atoms, 24 bonds, 1 residue, 1 model selected > renumber #5/A seqStart 26 527 residues renumbered > select add #5:142 31 atoms, 31 bonds, 2 residues, 1 model selected > hide ~sel > select ~sel 16807 atoms, 17247 bonds, 5 pseudobonds, 2084 residues, 10 models selected > hide sel & #5 cartoons > select #5/B:1@O29 1 atom, 1 residue, 1 model selected > select add #5/A:142@CG 2 atoms, 2 residues, 1 model selected > select #5/A:142@CG 1 atom, 1 residue, 1 model selected > select clear > select #5/A:142@CG 1 atom, 1 residue, 1 model selected > select add #5/B:1@O29 2 atoms, 2 residues, 1 model selected > distance #5/A:142@CG #5/B:1@O29 Distance between 1_holo_wt_pocket_aka_v4_model_0.cif #5/A ASP 142 CG and /B LIG1 1 O29: 6.647Å > show #!4 models > show #4.1 models > label (sel #5@O29 or :142@CG) atoms Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > select #5@O29 or :142@CG Expected a keyword > label (sel #5@O29 | :142@CG) atoms Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label atoms (sel #5@O29 | :142@CG) Expected a keyword > select #5@O29 | #4:142@CG 1 atom, 1 residue, 1 model selected > label sel atoms > select #5/A:142@CG 1 atom, 1 residue, 1 model selected > label sel atoms > select :142 32 atoms, 28 bonds, 4 residues, 4 models selected > label sel > save /Users/suhasgotla/Desktop/image1.png supersample 3 > open > /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/v5/boltz_results_v5/predictions/v5/v5_model_0.cif Summary of feedback from opening /Users/suhasgotla/Documents/ysl_postdoc/boltz/2_benchmarks_with_STRs/1_holo_templates/v5/boltz_results_v5/predictions/v5/v5_model_0.cif --- warning | Unable to fetch template for 'LIG1': will connect using distance criteria v5_model_0.cif title: . [more info...] Chain information for v5_model_0.cif #6 --- Chain | Description A | . Non-standard residues in v5_model_0.cif #6 --- LIG1 — (LIG1) No chain in structure corresponds to chain ID given in local score info (chain 'B') > rename #6 1_holo_wt_contact_aka_v5_model_0.cif > mmaker #6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 1_holo_wt_contact_aka_v5_model_0.cif, chain A (#6), sequence alignment score = 2545.1 RMSD between 469 pruned atom pairs is 0.904 angstroms; (across all 500 pairs: 1.132) > hide #!5 models > show #!1 models > show ligand > show zone ligand 4 protein res t Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show zone 4 ligand protein res t Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show zone 4 ligand #1&protein res t Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select zone 4 ligand #1&protein res t Missing or invalid ""near"" argument: invalid objects specifier > select zone ligand 4 #1&protein residues true Selected 147 atoms > select zone #1&ligand 4 #1&protein residues true Selected 103 atoms > show sel atoms > hide #6 models > show #6 models > hide sel cartoons > show sel cartoons > select add #1 4059 atoms, 4169 bonds, 3 pseudobonds, 502 residues, 4 models selected > select #6,1 & (ligand | :142) 62 atoms, 62 bonds, 1 pseudobond, 5 residues, 3 models selected > hide ~sel > select ~sel 21038 atoms, 21587 bonds, 5 pseudobonds, 2609 residues, 12 models selected > hide sel & #6#!1 cartoons > hide #!1 models Alignment identifier is 1/A Alignment identifier is 1 Alignment identifier is 3/A > select #6:142 8 atoms, 7 bonds, 1 residue, 1 model selected Alignment identifier is 6/A > renumber #6 seqStart 26 528 residues renumbered > select #6:142 8 atoms, 7 bonds, 1 residue, 1 model selected > show sel atoms > show sel cartoons Drag select of 5 atoms, 1 residues, 4 bonds > hide sel atoms > hide sel cartoons Drag select of 5 atoms, 1 residues, 4 bonds > label sel > select #6/A:142@CG 1 atom, 1 residue, 1 model selected > select add #6/B:26@O29 2 atoms, 2 residues, 1 model selected > label sel atoms > distance #6/A:142@CG #6/B:26@O29 Distance between 1_holo_wt_contact_aka_v5_model_0.cif #6/A ASP 142 CG and /B LIG1 26 O29: 6.248Å > view sel > save /Users/suhasgotla/Desktop/image1.png supersample 3 > show #!1 models > select add #1 4061 atoms, 4169 bonds, 3 pseudobonds, 504 residues, 5 models selected > hide #!6 models > select add #6 8321 atoms, 8542 bonds, 4 pseudobonds, 1030 residues, 6 models selected > select subtract #6 4059 atoms, 4169 bonds, 3 pseudobonds, 502 residues, 4 models selected > hide #4.1 models > show #4.1 models > view > select #1&ligand 23 atoms, 24 bonds, 2 residues, 1 model selected > style sel sphere Changed 23 atom styles > style sel sphere Changed 23 atom styles > style sel ball Changed 23 atom styles > style sel stick Changed 23 atom styles > save /Users/suhasgotla/Desktop/image1.png supersample 3 > show #!6 models > show #!5 models > show #4&ligand > select #4&ligand Nothing selected > show #5&ligand > hide #!1 models > show #5:142 > show #!1 models > hide #!5 models > hide #!6 models > select #1/C:2@C4 1 atom, 1 residue, 1 model selected > select add #1/C:2@C1 2 atoms, 1 residue, 1 model selected > select add #1/C:1@C2 3 atoms, 2 residues, 1 model selected > select add #1/C:1@C4 4 atoms, 2 residues, 1 model selected > show #!6 models > hide #!1 models > select #6/B:26@C36 1 atom, 1 residue, 1 model selected > select add #6/B:26@C34 2 atoms, 1 residue, 1 model selected > select add #6/B:26@C35 3 atoms, 1 residue, 1 model selected > select subtract #6/B:26@C35 2 atoms, 1 residue, 1 model selected > select add #6/B:26@C35 3 atoms, 1 residue, 1 model selected > select add #6/B:26@C39 4 atoms, 1 residue, 1 model selected > show #!1 models > hide #!4 models > show #!5 models > hide #!1 models > show #!1 models > hide #!6 models > hide #!5 models > select zone #1:rry 3.1 #1/A residues true Selected 22 atoms > info residues sel residue id #1/A:142 name ASP index 145 residue id #1/A:278 name ASP index 281 residue id #1/A:303 name SER index 306 > show sel > show sel cartoons > select zone #1:rrj 3.1 #1/A residues true Selected 23 atoms > show sel > show sel cartoons Drag select of 45 atoms, 5 residues, 41 bonds > info residues sel residue id #1/A:142 name ASP index 145 residue id #1/A:165 name SER index 168 residue id #1/A:278 name ASP index 281 residue id #1/A:302 name GLU index 305 residue id #1/A:303 name SER index 306 residue id #1/C:1 name RRY residue id #1/C:2 name RRJ > rmsd #6:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,103,142,143,165,277,278,302,303,306 RMSD between 103 atom pairs is 1.246 > rmsd #5:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,103,142,143,165,277,278,302,303,306 RMSD between 103 atom pairs is 1.184 > rmsd #3:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,103,142,143,165,277,278,302,303,306 Number of atoms from first atom spec (96) differs from number in second (103) > rmsd #3:40,65,67,71,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,142,143,165,277,278,302,303,306 RMSD between 91 atom pairs is 1.297 > rmsd #2:40,65,67,71,103,142,143,165,277,278,302,303,306 to > #1:40,65,67,71,103,142,143,165,277,278,302,303,306 RMSD between 103 atom pairs is 1.322 > mmaker #6 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 1_holo_wt_contact_aka_v5_model_0.cif, chain A (#6), sequence alignment score = 2545.1 RMSD between 469 pruned atom pairs is 0.904 angstroms; (across all 500 pairs: 1.132) > mmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 1_holo_wt_pocket_aka_v4_model_0.cif, chain A (#5), sequence alignment score = 2531.9 RMSD between 431 pruned atom pairs is 0.958 angstroms; (across all 500 pairs: 1.520) > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 1_holo_y103a_aka_v3_model_0.cif, chain A (#3), sequence alignment score = 2525.6 RMSD between 453 pruned atom pairs is 0.855 angstroms; (across all 500 pairs: 1.163) > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 9utc.pdb, chain A (#1) with 1_holo_wt_aka_v2_model_0.cif, chain A (#2), sequence alignment score = 2521.1 RMSD between 431 pruned atom pairs is 0.935 angstroms; (across all 500 pairs: 1.638) ===== Log before crash end ===== Log: 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 - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.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 Air Model Identifier: Mac15,12 Model Number: MXCU3LL/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.140.96 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.6.1 (24G90) Kernel Version: Darwin 24.6.0 Time since boot: 36 days, 10 hours, 15 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal VX2703 SERIES: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 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