id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17364 Crash closing dock widget chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-15.3.2-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 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 0x00000001fe49c840 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 52) {""app_name"":""ChimeraX"",""timestamp"":""2025-04-13 07:10:47.00 +0530"",""app_version"":""1.9.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.9.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":1,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 15.3.2 (24D81)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""B29BA178-6251-4F5B-AD86-59DEBB5971E4""} { ""uptime"" : 14000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro17,1"", ""coalitionID"" : 3462, ""osVersion"" : { ""train"" : ""macOS 15.3.2"", ""build"" : ""24D81"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2025-04-13 07:10:23.7525 +0530"", ""codeSigningMonitor"" : 1, ""incident"" : ""B29BA178-6251-4F5B-AD86-59DEBB5971E4"", ""pid"" : 6053, ""translated"" : false, ""cpuType"" : ""ARM-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2025-04-13 07:08:31.2062 +0530"", ""procStartAbsTime"" : 345231316517, ""procExitAbsTime"" : 347931286136, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.9.0"",""CFBundleVersion"":""1.9.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""EC4C023C-ED6F-5B02-9660-D431CC48E4E6"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""0B8C3D55-E7D9-FFA6-FF44-349177FD6221"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""instructionByteStream"" : {""beforePC"":""fyMD1f17v6n9AwCRcuD\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A=="",""atPC"":""AwEAVH8jA9X9e7+p\/QMAkWfg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g==""}, ""bootSessionUUID"" : ""811F8255-26A1-414B-B8D8-460CFBB1616B"", ""wakeTime"" : 5915, ""sleepWakeUUID"" : ""700E6451-C08C-477A-99DF-B25A8E596821"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0x41722cad3928 is not in any region. 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""f38c83a8b834cab168974c85841256820929bbf3"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64628732bf2f5257dedc8988"", ""factorPackIds"" : { }, ""deploymentId"" : 240000001 }, { ""rolloutId"" : ""654d8c0661e7447155256fcd"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""67edd39c73932228c9baf23a"" }, ""deploymentId"" : 240000307 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/abhishekdey/Downloads/fold_2025_04_03_09_58_model_4.cif Chain information for fold_2025_04_03_09_58_model_4.cif #1 --- Chain | Description A | . Computing secondary structure > open ""/Users/abhishekdey/Downloads/JEV simRNA 85.pdb"" Chain information for JEV simRNA 85.pdb #2 --- Chain | Description A | No description available Computing secondary structure > ui tool show Matchmaker > matchmaker #1 to #2/A pairing bs matrix Nucleic cutoffDistance 3.19 Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 | 3.19 Matchmaker JEV simRNA 85.pdb, chain A (#2) with fold_2025_04_03_09_58_model_4.cif, chain A (#1), sequence alignment score = 340 RMSD between 21 pruned atom pairs is 1.482 angstroms; (across all 85 pairs: 23.505) ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs Log from Fri Apr 11 06:08:41 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs Log from Fri Apr 11 05:44:17 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs Log from Thu Apr 10 17:10:03 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs Log from Thu Apr 10 16:52:14 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs Log from Thu Apr 10 06:59:20 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/abhishekdey/Downloads/7o7z.cif Summary of feedback from opening /Users/abhishekdey/Downloads/7o7z.cif --- warning | Unable to fetch template for 'SPD': will use incomplete information in mmCIF file notes | Fetching CCD 1MA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/1MA/1MA.cif Fetching CCD 2MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/2MG/2MG.cif Fetching CCD 4AC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/4AC/4AC.cif Fetching CCD 5MC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/5MC/5MC.cif Fetching CCD 5MU from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/5MU/5MU.cif Fetching CCD 6MZ from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/6MZ/6MZ.cif Fetching CCD A2M from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/A2M/A2M.cif Fetching CCD AAC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/AAC/AAC.cif Fetching CCD AME from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/E/AME/AME.cif Fetching CCD AYA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/AYA/AYA.cif Fetching CCD B8N from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/B8N/B8N.cif Fetching CCD G7M from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/G7M/G7M.cif Fetching CCD GTP from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/P/GTP/GTP.cif Fetching CCD H2U from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/H2U/H2U.cif Fetching CCD HIC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/HIC/HIC.cif Fetching CCD HY3 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/HY3/HY3.cif Fetching CCD M2G from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/M2G/M2G.cif Fetching CCD M3L from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/L/M3L/M3L.cif Fetching CCD MA6 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/MA6/MA6.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif Fetching CCD MLZ from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Z/MLZ/MLZ.cif Fetching CCD NMM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/NMM/NMM.cif Fetching CCD OMC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/OMC/OMC.cif Fetching CCD OMG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif Fetching CCD OMU from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/OMU/OMU.cif Fetching CCD SAC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/SAC/SAC.cif Fetching CCD SPM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/SPM/SPM.cif Fetching CCD UNX from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/X/UNX/UNX.cif Fetching CCD UR3 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/UR3/UR3.cif Fetching CCD UY1 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/1/UY1/UY1.cif Fetching CCD V5N from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/V5N/V5N.cif Fetching CCD YYG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/YYG/YYG.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 7o7z.cif title: Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a pseudoknot (classified for pseudoknot) [more info...] Chain information for 7o7z.cif #1 --- Chain | Description | UniProt A2 | 18S rRNA | AA | 40S ribosomal protein S27 | G1TZ76_RABIT 1-84 AB | Ribosomal protein S28 | G1TIB4_RABIT 1-69 AC | Ribosomal protein S27a | G1SK22_RABIT 1-156 AD | 40S ribosomal protein S30 | G1T8A2_RABIT 1-133 AE | Ribosomal protein eS26 | AF | RACK1 | G1SJB4_RABIT 1-317 AG | uS14 | G1U7M4_RABIT 1-56 AH | mRNA containing SARS-CoV-2 sequence | AI | E-site tRNA | AT | P-site Phe-tRNA(Phe) | AZ | 40S ribosomal protein SA | G1TLT8_RABIT 1-295 Aa | 40S ribosomal protein S3a | G1SS70_RABIT 1-264 Ab | Ribosomal protein uS5 | Ac | 40S ribosomal protein S3 | G1TNM3_RABIT -37-243 Ad | Ribosomal protein eS4 | Ae | Ribosomal protein S5 | G1TFM5_RABIT 1-204 Af | 40S ribosomal protein S6 | G1TM55_RABIT 1-249 Ag | 40S ribosomal protein S7 | G1SVB0_RABIT -237-194 Ah | 40S ribosomal protein S8 | G1TJW1_RABIT 1-208 Ai | Ribosomal protein S9 (Predicted) | B7NZS8_RABIT 1-194 Aj | eS10 | G1TPV3_RABIT 1-165 Ak | 40S ribosomal protein S11 | G1TRM4_RABIT 1-158 Al | 40S ribosomal protein S12 | G1SFR8_RABIT 1-132 Am | uS15 | G1SP51_RABIT 1-151 An | 40S ribosomal protein uS11 | G1T1F0_RABIT 1-151 Ao | 40S ribosomal protein uS19 | G1U0Q2_RABIT 1-145 Ap | uS9 | G1SGX4_RABIT -25-146 Aq | 40S ribosomal protein eS17 | G1TU13_RABIT 1-135 Ar | 40S ribosomal protein S18 | G1TPG3_RABIT 1-152 As | Ribosomal protein eS19 | At | 40S ribosomal protein uS10 | G1SIZ2_RABIT 1-119 Au | Ribosomal protein eS21 | Av | Ribosomal protein S15a | G1TG89_RABIT 1-130 Aw | 40S ribosomal protein S23 | G1SZ47_RABIT 1-143 Ax | 40S ribosomal protein S24 | G1T3D8_RABIT 1-130 Ay | 40S ribosomal protein S25 | G1TDB3_RABIT 2-125 Az | 60s ribosomal protein l41 | A0A087WNH4_RABIT 1-25 B5 | 28S rRNA | B7 | 5S | B8 | 5.8S rRNA | BA | Ribosomal protein uL2 | BB | Ribosomal protein L3 | G1TL06_RABIT 1-403 BC | 60S ribosomal protein L4 | G1SVW5_RABIT 1-413 BD | Ribosomal_L18_c domain-containing protein | G1SYJ6_RABIT 1-297 BE | 60S ribosomal protein L6 | G1SKF7_RABIT 1-291 BF | Ribosomal Protein uL30 | BG | Ribosomal protein eL8 | BH | 60S ribosomal protein L9 | G1SWI6_RABIT 1-192 BI | 60S ribosomal protein L10 | B7NZQ2_RABIT 1-214 BJ | Ribosomal protein L11 | G1TUB8_RABIT 1-178 BK | Replicase polyprotein 1ab | R1AB_SARS2 4254-5324 BL | Ribosomal protein eL13 | BM | Ribosomal protein L14 | G1SZ12_RABIT 1-218 BN | Ribosomal protein L15 | G1T0C1_RABIT 1-204 BO | Ribosomal protein uL13 | BP | uL22 | G1TVT6_RABIT 1-184 BQ | Ribosomal Protein eL18 | BR | 60S ribosomal protein L19 | RL19_BOVIN 1-196 BS | Ribosomal protein eL20 | BT | eL21 | G1SHQ2_RABIT 1-160 BU | Ribosomal protein eL22 | BV | Ribosomal protein L23 | G1T6D1_RABIT 1-140 BW | eL24 | G1SE28_RABIT 1-157 BX | uL23 | G1SE76_RABIT 1-156 BY | Ribosomal protein L26 | G1SQH0_RABIT 1-145 BZ | 60S ribosomal protein L27 | G1TXF6_RABIT 1-136 Ba | 60S ribosomal protein L27a | G1SNY0_RABIT 1-148 Bb | 60S ribosomal protein L29 | G1SGR6_RABIT 1-245 Bc | eL30 | G1TDL2_RABIT 1-115 Bd | eL31 | G1SHG0_RABIT 1-125 Be | eL32 | G1U437_RABIT 1-135 Bf | eL33 | G1SF08_RABIT 1-110 Bg | 60S ribosomal protein L34 | G1TXG5_RABIT 1-117 Bh | uL29 | G1SIT5_RABIT 1-123 Bi | 60S ribosomal protein L36 | G1TTQ5_RABIT 1-105 Bj | Ribosomal protein L37 | U3KPD5_RABIT 1-97 Bk | eL38 | G1U001_RABIT 1-70 Bl | eL39 | G1TTN1_RABIT 1-51 Bm | 60S ribosomal protein L40 | Bo | eL42 | G1U344_RABIT 1-106 Bp | eL43 | G1SY53_RABIT 1-92 Br | Ribosomal protein eL28 | Bs | 60S acidic ribosomal protein P0 | G1SPK4_RABIT 1-318 Bt | Ribosomal protein L12 | G1SMR7_RABIT 1-165 Bv | Ribosomal protein uL1 | G1SKZ8_RABIT 1-217 Non-standard residues in 7o7z.cif #1 --- AAC — acetylamino-acetic acid B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid GTP — guanosine-5'-triphosphate MG — magnesium ion SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) SPM — spermine UNX — unknown atom or ion UY1 — 2'-O-methylpseudouridine-5'-monophosphate ZN — zinc ion > show target m > select add #1 229742 atoms, 243775 bonds, 8384 pseudobonds, 21082 residues, 4 models selected > select subtract #1 Nothing selected > hide #!1 models > select add #1 229742 atoms, 243775 bonds, 8384 pseudobonds, 21082 residues, 4 models selected > show #!1 models > select subtract #1 Nothing selected > select add #1 229742 atoms, 243775 bonds, 8384 pseudobonds, 21082 residues, 4 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain /AH Alignment identifier is 1/AH > select clear > select /AH:3451-3545 2018 atoms, 2253 bonds, 67 pseudobonds, 95 residues, 2 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain /AH Alignment identifier is 1/AH > select clear > select /AH 2028 atoms, 2253 bonds, 70 pseudobonds, 105 residues, 3 models selected > cartoon (#!1 & sel) > surface hidePatches (#!1 & sel) > style (#!1 & sel) ball Changed 2028 atom styles > color (#!1 & sel) red OpenType support missing for "".AppleSystemUIFont"", script 11 > save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs ——— End of log from Thu Apr 10 06:59:20 2025 ——— opened ChimeraX session > open > /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_0.cif Chain information for fold_jevfse_115_2025_04_03_16_00_model_0.cif #2 --- Chain | Description A | . Computing secondary structure > select add #1 229742 atoms, 243775 bonds, 8384 pseudobonds, 21082 residues, 4 models selected > hide #!1 models > show #!1 models > select subtract #1 Nothing selected > ui tool show Matchmaker > matchmaker #2 to #1/AH pairing bs Using Nucleic matrix instead of BLOSUM-62 to match to 7o7z.cif #1/AH Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_0.cif, chain A (#2), sequence alignment score = 124.6 RMSD between 3 pruned atom pairs is 1.176 angstroms; (across all 95 pairs: 45.421) > open > /Users/abhishekdey/Downloads/fold_hiv_115_2025_04_03_17_20/fold_hiv_115_2025_04_03_17_20_model_4.cif Chain information for fold_hiv_115_2025_04_03_17_20_model_4.cif #3 --- Chain | Description A | . Computing secondary structure > open > /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_4.cif Chain information for fold_jevfse_115_2025_04_03_16_00_model_4.cif #4 --- Chain | Description A | . Computing secondary structure > hide #2 models > hide #3 models > show #2 models > open ""/Users/abhishekdey/Downloads/JEV115-ad5deff5_sim_minE_TOTAL-000001_AA > (2).pdb"" Chain information for JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb #5 --- Chain | Description A | No description available Computing secondary structure > ui tool show Matchmaker > matchmaker #5/A to #1/AH pairing ss Using Nucleic matrix instead of BLOSUM-62 to match JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb #5/A to 7o7z.cif #1/AH Computing secondary structure Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb, chain A (#5), sequence alignment score = 124.6 RMSD between 7 pruned atom pairs is 1.083 angstroms; (across all 95 pairs: 43.163) > ui tool show Matchmaker > hide #2 models > hide #4 models > hide #5 models > open /Users/abhishekdey/Downloads/fold_jev_5_100_model_4.cif format mmcif Chain information for fold_jev_5_100_model_4.cif #6 --- Chain | Description A | . Computing secondary structure > select add #6 2125 atoms, 2371 bonds, 100 residues, 1 model selected > color sel forest green > ui tool show Matchmaker > matchmaker #6 to #1/AH pairing bs Using Nucleic matrix instead of BLOSUM-62 to match to 7o7z.cif #1/AH Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jev_5_100_model_4.cif, chain A (#6), sequence alignment score = 103.6 RMSD between 6 pruned atom pairs is 0.649 angstroms; (across all 88 pairs: 51.930) > show #5 models > hide #5 models > show #4 models > select add #4 4574 atoms, 5104 bonds, 215 residues, 2 models selected > select subtract #4 2125 atoms, 2371 bonds, 100 residues, 1 model selected > show #3 models > hide #6 models > hide #3 models > show #3 models > select add #3 4586 atoms, 5126 bonds, 215 residues, 2 models selected > select add #4 7035 atoms, 7859 bonds, 330 residues, 3 models selected > cartoon (#3-4 & sel) > ui tool show Matchmaker > matchmaker #6 to #1/AH pairing bs matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jev_5_100_model_4.cif, chain A (#6), sequence alignment score = 103.6 RMSD between 6 pruned atom pairs is 0.649 angstroms; (across all 88 pairs: 51.930) > ui tool show Matchmaker > matchmaker #6 to #1/AH pairing bs matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jev_5_100_model_4.cif, chain A (#6), sequence alignment score = 103.6 RMSD between 6 pruned atom pairs is 0.649 angstroms; (across all 88 pairs: 51.930) > show #6 models > ui tool show Matchmaker > matchmaker #4 to #1/AH pairing bs matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment score = 124.6 RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs: 46.532) > matchmaker #4 to #1/AH pairing bs matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment score = 124.6 RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs: 46.532) > select subtract #6 4910 atoms, 5488 bonds, 230 residues, 2 models selected > select subtract #3 2449 atoms, 2733 bonds, 115 residues, 1 model selected > hide #3 models > select subtract #4 Nothing selected > hide #4 models > show #4 models > hide #6 models > ui tool show Matchmaker > matchmaker #4 to #1/AH pairing bs matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment score = 124.6 RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs: 46.532) > matchmaker #4 to #1/AH pairing bs matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment score = 124.6 RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs: 46.532) > matchmaker #4/A to #1/AH pairing ss matrix Nucleic Computing secondary structure Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#4), sequence alignment score = 124.6 RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs: 46.532) > hide #4 models > show #3 models > ui tool show Matchmaker > matchmaker #3/A to #1/AH pairing ss matrix Nucleic Computing secondary structure Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_hiv_115_2025_04_03_17_20_model_4.cif, chain A (#3), sequence alignment score = 121.4 RMSD between 6 pruned atom pairs is 1.123 angstroms; (across all 83 pairs: 65.777) > hide #!1 models > show #!1 models OpenType support missing for "".AppleSystemUIFont"", script 11 > save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs ——— End of log from Thu Apr 10 16:52:14 2025 ——— opened ChimeraX session > open > /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_2.cif > /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_3.cif Chain information for fold_jevfse_115_2025_04_03_16_00_model_2.cif #7 --- Chain | Description A | . Chain information for fold_jevfse_115_2025_04_03_16_00_model_3.cif #8 --- Chain | Description A | . Computing secondary structure [Repeated 1 time(s)] > hide #3 models > ui tool show Matchmaker > matchmaker #7/A to #1/AH pairing ss Using Nucleic matrix instead of BLOSUM-62 to match fold_jevfse_115_2025_04_03_16_00_model_2.cif #7/A to 7o7z.cif #1/AH Computing secondary structure Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7), sequence alignment score = 124.6 RMSD between 8 pruned atom pairs is 0.729 angstroms; (across all 95 pairs: 38.947) > hide #7 models > open > /Users/abhishekdey/Downloads/fold_jevfse_115_2025_04_03_16_00/fold_jevfse_115_2025_04_03_16_00_model_4.cif Chain information for fold_jevfse_115_2025_04_03_16_00_model_4.cif #9 --- Chain | Description A | . Computing secondary structure > ui tool show Matchmaker > matchmaker #8/A to #1/AH pairing ss Using Nucleic matrix instead of BLOSUM-62 to match fold_jevfse_115_2025_04_03_16_00_model_3.cif #8/A to 7o7z.cif #1/AH Computing secondary structure Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_3.cif, chain A (#8), sequence alignment score = 124.6 RMSD between 3 pruned atom pairs is 1.480 angstroms; (across all 95 pairs: 49.946) > hide #!1 models > show #!1 models > hide #8 models > show #7 models > hide #7 models > ui tool show Matchmaker > matchmaker #9/A to #1/AH pairing ss Using Nucleic matrix instead of BLOSUM-62 to match fold_jevfse_115_2025_04_03_16_00_model_4.cif #9/A to 7o7z.cif #1/AH Computing secondary structure Parameters --- Chain pairing | ss Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_jevfse_115_2025_04_03_16_00_model_4.cif, chain A (#9), sequence alignment score = 124.6 RMSD between 3 pruned atom pairs is 1.334 angstroms; (across all 95 pairs: 46.532) > hide #9 models > hide #!1 models > show #9 models > show #8 models > show #7 models > hide #8 models > hide #9 models > hide #7 models > show #8 models > show #9 models > delete atoms #8-9 > delete bonds #8-9 > show #7 models > show #!1 models > hide #7 models > show #5 models > hide #!1 models > show #!1 models > hide #5 models > hide #!1 models > show #4 models > delete atoms #4 > delete bonds #4 > show #2 models > delete atoms #2 > delete bonds #2 > show #!1 models > show #3 models > hide #3 models > hide #!1 models > show #6 models > delete atoms #6 > delete bonds #6 > show #7 models > show #5 models > show #3 models > show #!1 models OpenType support missing for "".AppleSystemUIFont"", script 11 > save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs ——— End of log from Thu Apr 10 17:10:03 2025 ——— opened ChimeraX session > hide #7 models > show #7 models > hide #3 models > hide #5 models > hide #!1 models > show #!1 models > select add #7 2449 atoms, 2733 bonds, 115 residues, 1 model selected > color sel forest green > select subtract #7 Nothing selected > show #5 models > ui tool show Matchmaker > matchmaker #5 to #7 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb, chain A (#5), sequence alignment score = 460 RMSD between 8 pruned atom pairs is 1.279 angstroms; (across all 115 pairs: 29.570) > matchmaker #5 to #7 Using Nucleic matrix instead of BLOSUM-62 for matching Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with JEV115-ad5deff5_sim_minE_TOTAL-000001_AA (2).pdb, chain A (#5), sequence alignment score = 460 RMSD between 8 pruned atom pairs is 1.279 angstroms; (across all 115 pairs: 29.570) > hide #!1 models > hide #7 models > show #!1 models > hide #5 models > show #7 models > color #3 #2020e1ff > color #3 #111174ff > color #3 #1b1dc7ff > color #3 #0c0d58ff > color #3 #101175ff > show #3 models OpenType support missing for "".AppleSystemUIFont"", script 11 > save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs ——— End of log from Fri Apr 11 05:44:17 2025 ——— opened ChimeraX session > open /Users/abhishekdey/Downloads/fold_2025_04_03_09_58_model_4.cif Chain information for fold_2025_04_03_09_58_model_4.cif #2 --- Chain | Description A | . Computing secondary structure > ui tool show Matchmaker > matchmaker #2 to #7 Using Nucleic matrix instead of BLOSUM-62 for matching Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with fold_2025_04_03_09_58_model_4.cif, chain A (#2), sequence alignment score = 340 RMSD between 26 pruned atom pairs is 1.006 angstroms; (across all 85 pairs: 26.431) > matchmaker #2 to #7 Using Nucleic matrix instead of BLOSUM-62 for matching Computing secondary structure Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with fold_2025_04_03_09_58_model_4.cif, chain A (#2), sequence alignment score = 340 RMSD between 26 pruned atom pairs is 1.006 angstroms; (across all 85 pairs: 26.431) > color #2 #eca185ff > color #2 #ec901cff > hide #!1 models > hide #3 models > hide #7 models > show #7 models > hide #2 models > show #2 models > show #!1 models > ui tool show Matchmaker > matchmaker #2 to #1/AH pairing bs Using Nucleic matrix instead of BLOSUM-62 to match to 7o7z.cif #1/AH Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 7o7z.cif, chain AH (#1) with fold_2025_04_03_09_58_model_4.cif, chain A (#2), sequence alignment score = 97.4 RMSD between 4 pruned atom pairs is 1.256 angstroms; (across all 82 pairs: 46.803) > ui tool show Matchmaker > matchmaker #2 to #7/A pairing bs matrix Nucleic Computing secondary structure Parameters --- Chain pairing | bs Alignment algorithm | Needleman-Wunsch Similarity matrix | Nucleic 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 fold_jevfse_115_2025_04_03_16_00_model_2.cif, chain A (#7) with fold_2025_04_03_09_58_model_4.cif, chain A (#2), sequence alignment score = 340 RMSD between 26 pruned atom pairs is 1.006 angstroms; (across all 85 pairs: 26.431) > hide #7 models > hide #!1 models > show #!1 models OpenType support missing for "".AppleSystemUIFont"", script 11 > save /Users/abhishekdey/Desktop/7o7z_SARSCoV2-FSE.cxs ——— End of log from Fri Apr 11 06:08:41 2025 ——— opened ChimeraX session OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYD92LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 11881.81.4 OS Loader Version: 11881.81.4 Software: System Software Overview: System Version: macOS 15.3.2 (24D81) Kernel Version: Darwin 24.3.0 Time since boot: 35 seconds Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 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: 2.3 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: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 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-MutationScores: 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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 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: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 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: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 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: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 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: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit can't reproduce Tom Goddard all ChimeraX