id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17737 Crash restoring many alignments from session 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. 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Libraries: Total=1.9G resident=0K(0%) swapped_out_or_unallocated=1.9G(100%)\nWritable regions: Total=16.0G written=8433K(0%) resident=8433K(0%) swapped_out=0K(0%) unallocated=16.0G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 128K 1 \nActivity Tracing 256K 1 \nCG image 576K 21 \nColorSync 640K 32 \nCoreAnimation 1888K 99 \nCoreGraphics 32K 2 \nCoreUI image data 5152K 39 \nFoundation 144K 3 \nKernel Alloc Once 32K 1 \nMALLOC 15.3G 149 \nMALLOC guard page 288K 18 \nMach message 64K 2 \nOpenGL GLSL 384K 4 \nSTACK GUARD 576K 36 \nStack 191.8M 37 \nStack Guard 56.0M 1 \nVM_ALLOCATE 256.5M 205 \nVM_ALLOCATE (reserved) 128.0M 4 reserved VM address space (unallocated)\n__AUTH 5284K 671 \n__AUTH_CONST 70.8M 919 \n__CTF 824 1 \n__DATA 33.5M 1069 \n__DATA_CONST 34.3M 1086 \n__DATA_DIRTY 2763K 342 \n__FONT_DATA 2352 1 \n__GLSLBUILTINS 5174K 1 \n__INFO_FILTER 8 1 \n__LINKEDIT 638.4M 161 \n__OBJC_RW 2374K 1 \n__TEXT 1.3G 1106 \n__TPRO_CONST 272K 2 \ndyld private memory 32K 2 \nmapped file 257.3M 58 \nowned unmapped memory 46.1M 1 \npage table in kernel 8433K 1 \nshared memory 3152K 21 \n=========== ======= ======= \nTOTAL 18.3G 6099 \nTOTAL, minus reserved VM space 18.2G 6099 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""09a0775d3319fcd8b3ccf737da550105b5e7a888"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""63508950b3714d3622fc77f7"", ""factorPackIds"" : { ""SIRI_MEMORY_SYNC_CONFIG"" : ""6526e111d0c9ce2f459b54a8"" }, ""deploymentId"" : 240000015 }, { ""rolloutId"" : ""6761d0c9df60af01adb250fb"", ""factorPackIds"" : { }, ""deploymentId"" : 240000009 } ], ""experiments"" : [ ] } } System Profile: Network Service: Wi-Fi, AirPort, en0 Thunderbolt Bus: MacBook Pro, Apple Inc. Thunderbolt Bus: MacBook Pro, Apple Inc. Boot Volume File System Type: apfs Memory Module: LPDDR5, Hynix USB Device: USB31Bus USB Device: USB31Bus Display: Color LCD, 3024 x 1964 Retina, Main, MirrorOff, Online Model: Mac15,3, BootROM 11881.81.4, proc 8:4:4 processors, 8 GB, SMC Graphics: Apple M3, Apple M3, Built-In AirPort: spairport_wireless_card_type_wifi (0x14E4, 0x4388), wl0: Oct 31 2024 06:18:43 version 23.10.900.20.41.51.176 FWID 01-24228154 IO80211_driverkit-1345.10 ""IO80211_driverkit-1345.10"" Dec 14 2024 17:47:07 AirPort: Bluetooth: Version (null), 0 services, 0 devices, 0 incoming serial ports ===== 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/evitatsiolaki/Downloads/run_it026_half1_class001.mrc Opened run_it026_half1_class001.mrc as #1, grid size 384,384,384, pixel 0.819, shown at level 0.0016, step 2, values float32 > close > open > /Users/evitatsiolaki/Dropbox/paper_Evita/Figures_All/new_fig_comparison/hHsp70_mutations_comparison.cxs > format session opened ChimeraX session > open /Users/evitatsiolaki/Downloads/run_it026_half1_class001.mrc Opened run_it026_half1_class001.mrc as #2, grid size 384,384,384, pixel 0.819, shown at level 0.0016, step 2, values float32 > ui mousemode right ""rotate selected models"" > select add #2 2 models selected > view matrix models > #2,0.19881,-0.97267,0.11991,267.78,0.59306,0.21681,0.77542,-86.524,-0.78023,-0.083043,0.61996,196.56 > view matrix models > #2,-0.86151,0.22485,-0.45525,327.45,-0.44064,0.11441,0.89037,74.622,0.25229,0.96765,0.00051086,-41.308 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.86151,0.22485,-0.45525,331.53,-0.44064,0.11441,0.89037,59.488,0.25229,0.96765,0.00051086,-43.591 > fitmap #1 inMap #2 Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1) to map run_it026_half1_class001.mrc (#2) using 18912 atoms average map value = 0.009092, steps = 148 shifted from previous position = 12.9 rotated from previous position = 13.7 degrees atoms outside contour = 525, contour level = 0.0015965 Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1) relative to run_it026_half1_class001.mrc (#2) coordinates: Matrix rotation and translation 0.02895178 0.21461974 -0.97626849 273.24994857 0.91288240 0.39218779 0.11328934 -55.59145916 0.40719471 -0.89449825 -0.18456805 259.76286793 Axis -0.54517417 -0.74840017 0.37773313 Axis point 39.22144795 0.00000000 235.71888993 Rotation angle (degrees) 112.43990677 Shift along axis -9.24311442 > volume #2 level 0.002463 > color #2 #fffc79ff models > color zone #2 near #1 distance 4.91 > select clear > volume #2 level 0.002959 > volume #2 level 0.003 > open > /Users/evitatsiolaki/Downloads/Masks/RELION_it010_half1_class001_region_116.mrc Failed opening file /Users/evitatsiolaki/Downloads/Masks/RELION_it010_half1_class001_region_116.mrc: MRC file is truncated. Failed reading 1 values, type int32 > open /Users/evitatsiolaki/Downloads/run_it025_class001.mrc Opened run_it025_class001.mrc as #3, grid size 384,384,384, pixel 0.819, shown at level 1.09e-06, step 2, values float32 > open /Users/evitatsiolaki/Downloads/run_it025_class002.mrc Opened run_it025_class002.mrc as #4, grid size 384,384,384, pixel 0.819, shown at level 2.01e-06, step 2, values float32 > open /Users/evitatsiolaki/Downloads/run_it025_class003.mrc Opened run_it025_class003.mrc as #5, grid size 384,384,384, pixel 0.819, shown at level 1.1e-06, step 2, values float32 > hide #!2 models > select add #3 2 models selected > select add #4 4 models selected > select add #5 6 models selected > view matrix models > #3,1,0,0,3.7366,0,1,0,-30.527,0,0,1,-20.302,#4,1,0,0,3.7366,0,1,0,-30.527,0,0,1,-20.302,#5,1,0,0,3.7366,0,1,0,-30.527,0,0,1,-20.302 > volume all level 0.1 > volume all level 0.04 > volume #3 level 0.02173 > volume #3 level 0.009598 > volume all level 0.01 > view matrix models > #3,1,0,0,-4.6811,0,1,0,-28.575,0,0,1,-7.8067,#4,1,0,0,-4.6811,0,1,0,-28.575,0,0,1,-7.8067,#5,1,0,0,-4.6811,0,1,0,-28.575,0,0,1,-7.8067 > ui mousemode right ""rotate selected models"" > view matrix models > #3,-0.77694,0.4611,-0.42866,258.91,-0.25819,0.38762,0.88492,-26.315,0.57419,0.79821,-0.18211,-42.528,#4,-0.77694,0.4611,-0.42866,258.91,-0.25819,0.38762,0.88492,-26.315,0.57419,0.79821,-0.18211,-42.528,#5,-0.77694,0.4611,-0.42866,258.91,-0.25819,0.38762,0.88492,-26.315,0.57419,0.79821,-0.18211,-42.528 > view matrix models > #3,-0.63859,0.75081,-0.1688,140.07,-0.074204,0.15825,0.98461,-29.916,0.76596,0.64128,-0.045342,-67.015,#4,-0.63859,0.75081,-0.1688,140.07,-0.074204,0.15825,0.98461,-29.916,0.76596,0.64128,-0.045342,-67.015,#5,-0.63859,0.75081,-0.1688,140.07,-0.074204,0.15825,0.98461,-29.916,0.76596,0.64128,-0.045342,-67.015 > hide #!4 models > hide #!5 models > fitmap #1 inMap #3 Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1) to map run_it025_class001.mrc (#3) using 18912 atoms average map value = 0.003121, steps = 516 shifted from previous position = 20.7 rotated from previous position = 50.3 degrees atoms outside contour = 17244, contour level = 0.01 Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1) relative to run_it025_class001.mrc (#3) coordinates: Matrix rotation and translation -0.08664378 0.27655191 -0.95708511 279.77064374 0.57727599 0.79690985 0.17800879 -51.41203834 0.81193922 -0.53707890 -0.22869405 153.62772861 Axis -0.37019722 -0.91581479 0.15568331 Axis point 83.82088737 0.00000000 184.55014492 Rotation angle (degrees) 105.02342814 Shift along axis -32.56913521 > hide #!3 models > hide #1 models > show #!2 models > show #!3 models > fitmap #3 inMap #2 Fit map run_it025_class001.mrc in map run_it026_half1_class001.mrc using 4436 points correlation = 0.8474, correlation about mean = 0.1091, overlap = 0.4952 steps = 140, shift = 13.1, angle = 20.2 degrees Position of run_it025_class001.mrc (#3) relative to run_it026_half1_class001.mrc (#2) coordinates: Matrix rotation and translation 0.92007490 -0.39062787 -0.02953057 88.03713042 0.39137813 0.91985419 0.02629516 -60.58876085 0.01689220 -0.03575114 0.99921795 3.06678271 Axis -0.07895578 -0.05907438 0.99512622 Axis point 192.91256946 185.83750897 0.00000000 Rotation angle (degrees) 23.13618782 Shift along axis -0.31996128 > hide #!3 models > show #!4 models > fitmap #4 inMap #2 Fit map run_it025_class002.mrc in map run_it026_half1_class001.mrc using 4324 points correlation = 0.8226, correlation about mean = 0.09163, overlap = 0.4463 steps = 152, shift = 5.82, angle = 15.3 degrees Position of run_it025_class002.mrc (#4) relative to run_it026_half1_class001.mrc (#2) coordinates: Matrix rotation and translation 0.87131427 -0.34580499 -0.34818150 149.07915961 0.36335536 0.93151543 -0.01587096 -56.01505290 0.32982470 -0.11268502 0.93729278 -22.73888766 Axis -0.09819992 -0.68771167 0.71931178 Axis point 207.05061259 356.19434669 -0.00000000 Rotation angle (degrees) 29.53424321 Shift along axis 7.52629405 > hide #!4 models > show #!5 models > fitmap #5 inMap #2 Fit map run_it025_class003.mrc in map run_it026_half1_class001.mrc using 4348 points correlation = 0.8328, correlation about mean = 0.01819, overlap = 0.4622 steps = 228, shift = 11.6, angle = 32 degrees Position of run_it025_class003.mrc (#5) relative to run_it026_half1_class001.mrc (#2) coordinates: Matrix rotation and translation 0.98538033 -0.16998159 0.01148316 34.59060775 0.17024111 0.98501269 -0.02771212 -26.37287744 -0.00660051 0.02926188 0.99954999 -4.81178440 Axis 0.16493461 0.05235061 0.98491420 Axis point 171.43962160 189.15346325 0.00000000 Rotation angle (degrees) 9.94582444 Shift along axis -0.41464233 > hide #!5 models > show #1 models > fitmap #1 inMap #2 Fit molecule HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1) to map run_it026_half1_class001.mrc (#2) using 18912 atoms average map value = 0.009092, steps = 392 shifted from previous position = 20.7 rotated from previous position = 50.3 degrees atoms outside contour = 11399, contour level = 0.01 Position of HSPA1A_phnx-R2_rsref_001_1monomer_isolde2-step1_dimer-ATP.pdb (#1) relative to run_it026_half1_class001.mrc (#2) coordinates: Matrix rotation and translation 0.02900610 0.21451632 -0.97628961 273.25960931 0.91288029 0.39219057 0.11329668 -55.60276150 0.40719556 -0.89452184 -0.18445180 259.76079826 Axis -0.54516979 -0.74838307 0.37777331 Axis point 39.21904168 -0.00000000 235.73561476 Rotation angle (degrees) 112.43453451 Shift along axis -9.23002082 > hide #!2 models > show #!3 models > color zone #3 near #1 distance 4.91 > hide #!3 models > show #!4 models > color zone #4 near #1 distance 4.91 > show #!5 models Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic models, 2 maps. > volume all color #fffc79 > hide #!4 models > color zone #5 near #1 distance 4.91 > hide #!5 models > show #!4 models > color zone #4 near #1 distance 4.91 > hide #!4 models > show #!3 models > color zone #3 near #1 distance 4.91 > hide #1 models > show #!4 models > show #!5 models > tile 3 models tiled > volume all level 0.01 > volume all level 0.005 > hide #!4 models > hide #!3 models > show #!4 models > show #!3 models > select subtract #4 4 models selected > select subtract #3 2 models selected > view matrix models > #5,0.56306,0.8253,-0.042966,-49.8,-0.015777,0.062715,0.99791,-135.34,0.82627,-0.5612,0.048333,129.54 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.56306,0.8253,-0.042966,-47.204,-0.015777,0.062715,0.99791,-17.523,0.82627,-0.5612,0.048333,-99.471 > view matrix models > #5,0.56306,0.8253,-0.042966,-47.668,-0.015777,0.062715,0.99791,-14.832,0.82627,-0.5612,0.048333,-100.43 > select clear > open > /Users/evitatsiolaki/Documents/ChimeraSessions/ChimeraSessions/Model_Angelo_noseq_prediction.cxs restore_snapshot for ""Volume"" returned None restore_snapshot for ""VolumeSurface"" returned None restore_snapshot for ""Redust"" returned None opened ChimeraX session Alignment identifier is 2/A Alignment identifier is 2/B Alignment identifier is 2/C Alignment identifier is 2/E Alignment identifier is 2/F Alignment identifier is 2/G Alignment identifier is 2/H Alignment identifier is 2/I Alignment identifier is 1 Alignment identifier is 2/K Alignment identifier is 2/L Alignment identifier is 2/M Alignment identifier is 2 Alignment identifier is 2/R Alignment identifier is 2/S Alignment identifier is 2/T Alignment identifier is 3 Alignment identifier is 2/V Alignment identifier is 2/W Alignment identifier is 2/X Alignment identifier is 2/Z Alignment identifier is 2/c Alignment identifier is 2/e Alignment identifier is 2/f Alignment identifier is 2/g Alignment identifier is 4 Alignment identifier is 2/k Alignment identifier is 5 Alignment identifier is 2/p Alignment identifier is 6 Alignment identifier is 2/u Alignment identifier is 7 Alignment identifier is 2/y Alignment identifier is 2/1 Alignment identifier is 2/2 Alignment identifier is 2/8 Alignment identifier is 2/9 Alignment identifier is 2/AA Alignment identifier is 2/AC Alignment identifier is 2/AF Alignment identifier is 2/AG Alignment identifier is 2/AL Alignment identifier is 2/AN Alignment identifier is 2/AO Alignment identifier is 8 Alignment identifier is 2/AS Alignment identifier is 2/AT Alignment identifier is 2/AU Alignment identifier is 2/AW Alignment identifier is 2/AX Alignment identifier is 2/AZ Alignment identifier is 2/Ac Alignment identifier is 2/Am Alignment identifier is 2/An Alignment identifier is 2/Ao Alignment identifier is 2/As Alignment identifier is 2/Ay Alignment identifier is 2/A0 Alignment identifier is 2/A1 Alignment identifier is 2/A5 Alignment identifier is 2/BA Alignment identifier is 2/BM Alignment identifier is 2/BO Alignment identifier is 2/Bj Alignment identifier is 2/Bo Alignment identifier is 2/Bq Alignment identifier is 2/Br Alignment identifier is 2/Bs Alignment identifier is 2/Bt Alignment identifier is 2/Bu Alignment identifier is 2/Bv Alignment identifier is 2/Bw Alignment identifier is 2/Bx Alignment identifier is 2/By Alignment identifier is 2/Bz Alignment identifier is 2/B0 Alignment identifier is 2/B1 Alignment identifier is 2/B2 Alignment identifier is 2/B3 Alignment identifier is 2/B4 Alignment identifier is 2/B5 Alignment identifier is 2/B6 Alignment identifier is 2/B7 Alignment identifier is 2/B8 Alignment identifier is 2/B9 Alignment identifier is 2/CA Alignment identifier is 2/CB Alignment identifier is 2/CC Alignment identifier is 2/CD Alignment identifier is 2/CE Alignment identifier is 2/CF Alignment identifier is 2/CG Alignment identifier is 2/CH Alignment identifier is 2/CI Alignment identifier is 2/CJ Alignment identifier is 2/CK Alignment identifier is 2/CL Alignment identifier is 2/CM Alignment identifier is 2/CN Alignment identifier is 2/CO Alignment identifier is 2/CP Alignment identifier is 2/CQ Alignment identifier is 2/CR Alignment identifier is 2/CS Alignment identifier is 2/CT Alignment identifier is 2/CV Alignment identifier is 2/CW Alignment identifier is 2/CX Alignment identifier is 2/CY Alignment identifier is 2/CZ Alignment identifier is 2/Ca Alignment identifier is 2/Cb Alignment identifier is 2/Cc Alignment identifier is 2/Cd Alignment identifier is 2/Ce Alignment identifier is 2/Cf Alignment identifier is 2/Cg Alignment identifier is 2/Ch Alignment identifier is 2/Ci Alignment identifier is 2/Cj Alignment identifier is 2/Ck Alignment identifier is 2/Cl Alignment identifier is 2/Cm Alignment identifier is 2/Cn Alignment identifier is 2/Co Alignment identifier is 2/Cp Alignment identifier is 2/Cq Alignment identifier is 2/Cr Alignment identifier is 2/Cs Alignment identifier is 2/Ct Alignment identifier is 2/Cu Alignment identifier is 2/Cv Alignment identifier is 2/Cw Alignment identifier is 2/Cx Alignment identifier is 2/Cy Alignment identifier is 2/Cz Alignment identifier is 2/C0 Alignment identifier is 2/C1 Alignment identifier is 2/C2 ===== Log before crash end ===== Log: 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/evitatsiolaki/Downloads/volumes/volume_half1_000.mrc Opened volume_half1_000.mrc as #1, grid size 192,192,192, pixel 0.819, shown at level 35, step 1, values float32 OpenGL version: 4.1 Metal - 89.3 OpenGL renderer: Apple M3 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: Mac15,3 Model Number: MR7K3LL/A Chip: Apple M3 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: 21 days, 6 hours, 9 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 XDR Display Resolution: 3024 x 1964 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-NIHPresets: 1.2.7 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-StarMap: 1.2.15 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 pyqtgraph: 0.13.7 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 Sessions can't reproduce all ChimeraX