id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10387 Crash in garbage collection saving session ogahura@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-12.4-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 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 0x0000000117a95600 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molobject.py"", line 2000 in save_state File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 219 in take_snapshot File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 1417 in take_snapshot File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 296 in process File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 273 in discovery File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 636 in save File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py"", line 912 in save File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py"", line 95 in save File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 101 in provider_save File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/cmd.py"", line 86 in cmd_save File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py"", line 49 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 62 in display File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 138 in show_save_file_dialog File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/save_command/dialog.py"", line 127 in File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, 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scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize.__nnls, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, scipy.optimize._direct, chimerax.alignment_algs._sw, chimerax.alignment_algs._nw (total: 119) {""app_name"":""ChimeraX"",""timestamp"":""2023-12-21 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""\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.0"",""CFBundleVersion"":""1.7.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""D77DF969-7497-5E85-83B5-874A6142407E"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""1A6806F6-AE08-11C2-BA1A-F633BED1665C"", ""wakeTime"" : 25618, ""bridgeVersion"" : {""build"":""19P5071"",""train"":""6.5""}, ""sleepWakeUUID"" : ""B17C9B5B-0741-4589-B574-E45874D145F3"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. 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unallocated=22.3G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 512K 4 \nActivity Tracing 256K 1 \nCG backing stores 2160K 4 \nCG image 952K 46 \nColorSync 240K 28 \nCoreAnimation 1176K 25 \nCoreGraphics 12K 2 \nCoreServices 624K 2 \nCoreUI image data 4820K 35 \nFoundation 40K 2 \nKernel Alloc Once 8K 1 \nMALLOC 21.2G 972 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 384K 1 reserved VM address space (unallocated)\nMALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated)\nMach message 16K 2 \nObjC additional data 15K 1 \nOpenGL GLSL 384K 4 \nSTACK GUARD 128K 32 \nStack 166.8M 33 \nStack Guard 56.0M 1 \nVM_ALLOCATE 461.3M 475 \nVM_ALLOCATE (reserved) 96.0M 2 reserved VM address space (unallocated)\n__CTF 756 1 \n__DATA 49.3M 747 \n__DATA_CONST 32.6M 344 \n__DATA_DIRTY 1641K 213 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 688.7M 219 \n__TEXT 904.4M 744 \n__UNICODE 592K 1 \ndyld private memory 1184K 3 \nmapped file 491.2M 66 \nshared memory 2972K 24 \n=========== ======= ======= \nTOTAL 24.5G 4046 \nTOTAL, minus reserved VM space 24.1G 4046 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""60da5e84ab0ca017dace9abf"", ""factorPackIds"" : { }, ""deploymentId"" : 240000008 }, { ""rolloutId"" : ""61af99aeda72d16a4beb7756"", ""factorPackIds"" : { ""SIRI_DIALOG_ASSETS"" : ""6369252eff18954a57eb0bf4"" }, ""deploymentId"" : 240000409 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/mS22.cxs > format session opened ChimeraX session Chains must have same sequence > info selection level residue residue id #1.8/AD:369 name HIS index 281 > ui tool show ""Show Sequence Viewer"" > sequence chain #1.8/AD Chains must have same sequence > select #1.22/AR:114 10 atoms, 9 bonds, 1 residue, 1 model selected Alignment identifier is 1.22/AR > select #1.8/AD:370 16 atoms, 15 bonds, 1 residue, 1 model selected Chains must have same sequence > select #1.8/AD:362 19 atoms, 18 bonds, 1 residue, 1 model selected Chains must have same sequence > select #1.22/AR:104 22 atoms, 21 bonds, 1 residue, 1 model selected > hide #!5 models > show #!5 models > select add #5.18/Ca:357 28 atoms, 26 bonds, 2 residues, 2 models selected Destroying pre-existing alignment with identifier 1.22/AR Alignment identifier is 1.22/AR Alignment identifier is 5.18/Ca > select #1.22/AR:101 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1.22/AR:101 14 atoms, 14 bonds, 1 residue, 1 model selected > select add #5.18/Ca:354 21 atoms, 20 bonds, 2 residues, 2 models selected > select sequence PYRFLQTE 74 atoms, 76 bonds, 8 residues, 1 model selected > select #1.22/AR:101 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1.22/AR:101 14 atoms, 14 bonds, 1 residue, 1 model selected > select #1.22/AR:101-102 28 atoms, 28 bonds, 2 residues, 1 model selected > select #1.22/AR:101-105 90 atoms, 91 bonds, 5 residues, 1 model selected > hide #!5 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!4 models > hide #!3 models > show #!3 models > hide #!4 models > show #!5 models > hide #!5 models > hide #!3 models > show #!1 models > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > select clear > ui tool show ""Side View"" > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_Hs.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!1 models > show #!2 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_Sc.png > width 3000 height 2182 supersample 3 transparentBackground true > show #!3 models > hide #!2 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_At.png > width 3000 height 2182 supersample 3 transparentBackground true > view name 5_22 > show #!5 models > hide #!3 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_Tb.png > width 3000 height 2182 supersample 3 transparentBackground true > view 5_22 > show #!6 models > hide #!5 models > show #!4 models > hide #!6 models > show #!1 models > hide #!1 models > show #!1 models > view 5_22 > hide #!4 models > show #!4 models > hide #!1 models > ~ribbon #4.41 > view 5_22 > show #!1 models > hide #!1 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_22_Tt.png > width 3000 height 2182 supersample 3 transparentBackground true > view default > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/mS22.cxs > ribbon #4.41 > hide #!4 models > show #!1 models > hide #!1 models > show #!3 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!4 models > show #!5 models > hide #!4 models > show #!1 models > hide #!5 models > hide #!1 models > show #!2 models > show #!1 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > hide #!1 models Drag select of 135 residues > dssp sel > dssp sel energyCutoff -0.1 > hide #!3 models > show #!1 models > show #!2 models > hide #!1 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > view name S16_22 > show #!1 models > hide #!5 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S16_22_Hs.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!1 models > show #!2 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S16_22_Sc.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!2 models > show #!3 models > select clear > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_16_At.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!3 models > show #!4 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S16_22_Tt.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!4 models > show #!5 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S16_22_Tb.png > width 3000 height 2182 supersample 3 transparentBackground true > view default > show #!1 models > hide #!5 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!3 models > hide #!1 models > view S5_22 Expected an objects specifier or a view name or a keyword > view 5_22 > view default > hide #!3 models > show #!4 models > show #!6 models > hide #!4 models > view default > surface #6 > ~surface #6.5,16 > silhouette afda Unknown command: silhouette afda > sillhouete afda Unknown command: sillhouete afda > silhouettes fads Unknown command: silhouettes fads > silhouette fads Unknown command: silhouette fads > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting soft > graphics silhouettes width 1 > graphics silhouettes width 2 > graphics silhouettes width 3 > graphics silhouettes width 2 > graphics silhouettes width 3 > graphics silhouettes Current silhouette settings: enabled: True width: 3 color: 0,0,0 depth jump: 0.03 > graphics silhouettes Current silhouette settings: enabled: True width: 3 color: 0,0,0 depth jump: 0.03 > graphics silhouettes width 2 > graphics silhouettes width 2 depthJump 0.1 > graphics silhouettes width 2 depthJump 0.06 > view default > graphics silhouettes width 2 depthJump 0.03 > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig._mS22/S5_16_22_silhouetteEc.png > width 3000 height 2182 supersample 3 transparentBackground true > close session > open ""/Users/ondrejgahura/Work/Lab > Book/Mitoribosomes/_LECA_mitoribosome/Structure_analyses/mtSSU_start.cxs"" > format session opened ChimeraX session > hide #!10 models > hide #!11 models > select add #6.13 909 atoms, 900 bonds, 133 residues, 1 model selected > show #!1 models > ribbon #1 > show #!2 models > hide #!2 models > ribbon #1-6 > show #!2 models > hide #!2 models > show #!3 models > hide #!3 models > show #!4 models > hide #!4 models > show #!5 models > hide #!5 models > show #!5 models > hide #!5 models > show #!5 models > hide #!1 models > hide #!6 models > show #!6 models > hide #!5 models > show #!5 models > hide #!5 models > select add #6.19 1601 atoms, 1585 bonds, 241 residues, 2 models selected > show #!5 models > close #7-11 > close #2,4 > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs > hide #!5 models > show #!1 models > hide #!1 models > show #!1 models > show #!3 models > show #!5 models > color dimgrey > hide #!5 models > hide #!3 models > hide #!1 models > color name c4 #FC7300 Color 'c4' is opaque: rgb(98.8%, 45.1%, 0%) hex: #fc7300 > color #6.13#3.29 > color #6.13#3.29 c4 > select clear > lighting simple > lighting soft > show #!1 models > hide #!6 models > select #1.5/AA:5080 18 atoms, 19 bonds, 1 residue, 1 model selected > select add #1.5/AA:5087 39 atoms, 42 bonds, 2 residues, 1 model selected > select add #1.10/AF:311 60 atoms, 65 bonds, 3 residues, 2 models selected > select add #1.10/AF:320 81 atoms, 88 bonds, 4 residues, 2 models selected > select add #1.10/AF:305 102 atoms, 111 bonds, 5 residues, 2 models selected > select add #1.10/AF:301 123 atoms, 134 bonds, 6 residues, 2 models selected Alignment identifier is 1.5/AA Chains must have same sequence > select #1.5/AA:5047 18 atoms, 19 bonds, 1 residue, 1 model selected > select #1.5/AA:5047-5078,5080-5087 772 atoms, 865 bonds, 40 residues, 1 model selected > ~ribbon sel > select #1.10/AF:311 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #1.10/AF:170 37 atoms, 38 bonds, 2 residues, 1 model selected > select add #1.10/AF:301 58 atoms, 61 bonds, 3 residues, 1 model selected > select add #1.10/AF:319 76 atoms, 80 bonds, 4 residues, 1 model selected Chains must have same sequence Chains must have same sequence > select add #1.10/AF:312 97 atoms, 103 bonds, 5 residues, 1 model selected > select add #1.10/AF:313 119 atoms, 127 bonds, 6 residues, 1 model selected > select add #1.10/AF:314 140 atoms, 150 bonds, 7 residues, 1 model selected > select add #1.10/AF:303 158 atoms, 169 bonds, 8 residues, 1 model selected > select subtract #1.10/AF:303 140 atoms, 150 bonds, 7 residues, 1 model selected > select add #1.10/AF:302 161 atoms, 173 bonds, 8 residues, 1 model selected > select add #1.10/AF:303 179 atoms, 192 bonds, 9 residues, 1 model selected > select add #1.10/AF:304 200 atoms, 215 bonds, 10 residues, 1 model selected > select add #1.10/AF:305 221 atoms, 238 bonds, 11 residues, 1 model selected > select subtract #1.10/AF:170 205 atoms, 223 bonds, 10 residues, 1 model selected > select add #1.10/AF:317 223 atoms, 242 bonds, 11 residues, 1 model selected > select add #1.10/AF:316 241 atoms, 261 bonds, 12 residues, 1 model selected > select add #1.10/AF:318 259 atoms, 280 bonds, 13 residues, 1 model selected > select add #1.10/AF:315 277 atoms, 299 bonds, 14 residues, 1 model selected > select add #1.10/AF:320 298 atoms, 322 bonds, 15 residues, 1 model selected > delete sel > select #1.10/AF:306 21 atoms, 23 bonds, 1 residue, 1 model selected > select add #1.10/AF:310 39 atoms, 42 bonds, 2 residues, 1 model selected > select add #1.10/AF:309 57 atoms, 61 bonds, 3 residues, 1 model selected > select add #1.10/AF:308 78 atoms, 84 bonds, 4 residues, 1 model selected > select add #1.10/AF:307 99 atoms, 107 bonds, 5 residues, 1 model selected > delete sel > show #!5 models > hide #!5 models > show #!6 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs > show #!5 models > hide #!1 models > select #5.54/DX:52 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 291 atoms, 298 bonds, 34 residues, 1 model selected > select up 1196 atoms, 1231 bonds, 141 residues, 1 model selected > select down 291 atoms, 298 bonds, 34 residues, 1 model selected > select up 1196 atoms, 1231 bonds, 141 residues, 1 model selected > select down 291 atoms, 298 bonds, 34 residues, 1 model selected > select up 1196 atoms, 1231 bonds, 141 residues, 1 model selected > select up 177122 atoms, 182802 bonds, 20809 residues, 63 models selected > select down 1196 atoms, 1231 bonds, 141 residues, 1 model selected > select up 177122 atoms, 182802 bonds, 20809 residues, 63 models selected > select down 1196 atoms, 1231 bonds, 141 residues, 1 model selected > color name c2 #1F8A70 Color 'c2' is opaque: rgb(12.2%, 54.1%, 43.9%) hex: #1f8a70 > color name c3 #BFDB38 Color 'c3' is opaque: rgb(74.9%, 85.9%, 22%) hex: #bfdb38 > color name c1 #00425A Color 'c1' is opaque: rgb(0%, 25.9%, 35.3%) hex: #00425a > color sel c2 > select #5.32/DB:1151 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 30 atoms, 31 bonds, 3 residues, 1 model selected > select up 9148 atoms, 9369 bonds, 1111 residues, 1 model selected > color sel c3 > hide #!5 models > show #!1 models > hide #!1 models > show #!1 models > select clear > select add #1 120930 atoms, 124301 bonds, 913 pseudobonds, 6512 residues, 44 models selected > show sel atoms > hide sel atoms > color sel white > select clear > select #6.13/M:58 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 139 atoms, 138 bonds, 18 residues, 1 model selected > select up 891 atoms, 900 bonds, 115 residues, 1 model selected > surface sel > transparency sel 80 surfaces > select clear > show #!5 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select #5 177122 atoms, 182802 bonds, 293 pseudobonds, 20809 residues, 91 models selected > select subtract #5/DB,DX 166778 atoms, 172202 bonds, 293 pseudobonds, 19557 residues, 89 models selected > color sel white > hide #!1 models > show #!1 models > cartoon style xsection barbell barSides 18 barScale 0.4 thickness 0.8 width > 3 > select clear > lighting soft > lighting simple > color name p2_1 #557B83 Color 'p2_1' is opaque: rgb(33.3%, 48.2%, 51.4%) hex: #557b83 > color name p2_2 #39AEA9 Color 'p2_2' is opaque: rgb(22.4%, 68.2%, 66.3%) hex: #39aea9 > color name p2_3 #A2D5AB Color 'p2_3' is opaque: rgb(63.5%, 83.5%, 67.1%) hex: #a2d5ab > color name p2_4 #E5EFC1 Color 'p2_4' is opaque: rgb(89.8%, 93.7%, 75.7%) hex: #e5efc1 > hide #!5 models > select #6.13 909 atoms, 900 bonds, 133 residues, 1 model selected > transparency surface 40 sel Missing or invalid ""percent"" argument: Expected a number > transparency sel 40 surfaces > select clear > undo > ~ribbon sel > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!5 models > cartoon style modeHelix tube > hide #!5 models > lighting soft > lighting simple > ribbon sel > ~surface sel > surface sel > ~ribbon sel > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > view name side > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs > select clear > view side > show #!1 models > hide #!1 models > lighting soft > view side > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs > lighting flat > show #!1 models > view name side > lighting soft > lighting flat > view side > lighting soft > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_Hs_soft.png > width 3000 height 2182 supersample 3 transparentBackground true > lighting flat > view side > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_Hs_flat.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!1 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_flat.png > width 3000 height 2182 supersample 3 transparentBackground true > lighting soft > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_soft.png > width 3000 height 2182 supersample 3 transparentBackground true > show #!1 models > view side > turn y 180 > turn y 90 > lighting simple > view name v1 > lighting flat > lighting soft > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_Ec_Hs_soft.png > width 3000 height 2182 supersample 3 transparentBackground true > lighting flat > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_Ec_Hs_flat.png > width 3000 height 2182 supersample 3 transparentBackground true > select #6.13 909 atoms, 900 bonds, 133 residues, 2 models selected > cofr sel > turn y 180 > select clear > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_180_Ec_Hs_flat.png > width 3000 height 2182 supersample 3 transparentBackground true > lighting full > lighting soft > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_180_Ec_Hs_soft.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!1 models > lighting simple > show #!5 models > select #6.13 909 atoms, 900 bonds, 133 residues, 2 models selected > ribbon sel > ~surface sel > select clear > show #!1 models > cartoon style modeHelix default > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/uS13m.cxs > hide #!1 models > ui mousemode right ""translate selected models"" > select add #5 177122 atoms, 182802 bonds, 293 pseudobonds, 20809 residues, 91 models selected > view matrix models #5,1,0,0,6.2984,0,1,0,-2.2598,0,0,1,8.7731 > view matrix models #5,1,0,0,9.7859,0,1,0,-4.6402,0,0,1,12.578 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.9988,0.043722,0.022017,-6.2406,-0.044176,0.99881,0.020583,0.81371,-0.021091,-0.02153,0.99955,22.942 > select #5.54/DX:62 5 atoms, 4 bonds, 1 residue, 1 model selected > select up 291 atoms, 298 bonds, 34 residues, 1 model selected > select up 1196 atoms, 1231 bonds, 141 residues, 1 model selected > cofr sel > select clear > select add #5 177122 atoms, 182802 bonds, 293 pseudobonds, 20809 residues, 91 models selected > view matrix models > #5,0.99794,0.061826,0.017323,-9.811,-0.062556,0.99701,0.045329,-0.1011,-0.014468,-0.046319,0.99882,28.197 > view matrix models > #5,0.99602,0.04647,0.076047,-18.054,-0.055751,0.99061,0.12486,-17.14,-0.06953,-0.1286,0.98926,64.156 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.99602,0.04647,0.076047,-15.098,-0.055751,0.99061,0.12486,-12.648,-0.06953,-0.1286,0.98926,60.795 > view matrix models > #5,0.99602,0.04647,0.076047,-13.368,-0.055751,0.99061,0.12486,-9.9377,-0.06953,-0.1286,0.98926,58.347 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.99602,0.046484,0.076057,-13.371,-0.055765,0.99061,0.12485,-9.9321,-0.069539,-0.12859,0.98926,58.348 > view matrix models > #5,0.99109,8.5388e-06,0.13322,-12.203,-0.016383,0.99242,0.12181,-18.402,-0.13221,-0.12291,0.98357,71.807 > ui mousemode right ""translate selected models"" > view matrix models > #5,0.99109,8.5388e-06,0.13322,-11.851,-0.016383,0.99242,0.12181,-18.731,-0.13221,-0.12291,0.98357,73.319 > view matrix models > #5,0.99109,8.5388e-06,0.13322,-12.636,-0.016383,0.99242,0.12181,-19.432,-0.13221,-0.12291,0.98357,73.029 > view matrix models > #5,0.99109,8.5388e-06,0.13322,-11.673,-0.016383,0.99242,0.12181,-18.653,-0.13221,-0.12291,0.98357,72.01 > hide #!5 models > show #!5 models > select clear > ui mousemode right select Drag select of 1028 residues Drag select of 80 residues Drag select of 831 residues Drag select of 205 residues > select clear > color #5.32 paleblue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #5.32 lightblue > color list 8 custom colors: c1 , c2 , c3 , c4 , p2_1 , p2_2 , p2_3 , and p2_4 . 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color #5.54 pink > ui tool show ""Build Structure"" > color #5.54 lemonchiffon > lighting soft > lighting simple > select #5.32/DB:1163 9 atoms, 8 bonds, 1 residue, 1 model selected > select add #5.32/DB:1130 20 atoms, 19 bonds, 2 residues, 1 model selected Alignment identifier is 5.32/DB > select #5.32/DB:1130 11 atoms, 11 bonds, 1 residue, 1 model selected > select #5.32/DB:1130-1163 273 atoms, 279 bonds, 34 residues, 1 model selected > color sel royalblue > select #5.54/DX:74 6 atoms, 5 bonds, 1 residue, 1 model selected > select add #5.54/DX:37 15 atoms, 13 bonds, 2 residues, 1 model selected Alignment identifier is 5.54/DX > select #5.54/DX:37 9 atoms, 8 bonds, 1 residue, 1 model selected > select #5.54/DX:37-74 320 atoms, 327 bonds, 38 residues, 1 model selected > color sel tan > color sel salmon > color sel khaki > color sel olive > color sel gold > color sel mediumvioletred > color #5.54 lightpink > color sel mediumvioletred > view v1 > undo Drag select of 207 residues Drag select of 18 residues > select #6 54421 atoms, 56148 bonds, 1975 pseudobonds, 6431 residues, 30 models selected > select subtract #6.13 53512 atoms, 55248 bonds, 1975 pseudobonds, 6298 residues, 29 models selected > hide sel & #6.2-12,14-21#!6.1 cartoons > hide #!5 models > show sel & #6.2-12,14-21#!6.1 atoms > show #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > hide #!6 models Drag select of 14 residues > show #!6 models > hide #!5 models > show #!5 models > hide #!6 models > select #5 177122 atoms, 182802 bonds, 293 pseudobonds, 20809 residues, 91 models selected > select subtract #5.32,54 166778 atoms, 172202 bonds, 293 pseudobonds, 19557 residues, 89 models selected > hide sel cartoons > show sel atoms > hide #!5 models > show #!6 models > show #!5 models > hide #!6 models > transparency sel 100 > transparency sel 100 atoms > transparency sel 50 atoms > lighting soft > lighting flat > lighting soft > lighting simple > hide sel atoms > surface sel > transparency sel 80 surfaces > transparency sel 50 surfaces > lighting soft > show #!6 models > hide #!6 models > lighting flat > lighting soft > select #5.7/CJ:614@CG 1 atom, 1 residue, 1 model selected > select clear > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/Tb_S13.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!5 models > show #!6 models > select #6 54421 atoms, 56148 bonds, 1975 pseudobonds, 6431 residues, 29 models selected > show #!5 models > view name v2 > hide #!6 models > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/Tb_S13.png > width 3000 height 2182 supersample 3 transparentBackground true > show #!6 models > hide #!5 models > select subtract #6.13 53512 atoms, 55248 bonds, 1975 pseudobonds, 6298 residues, 29 models selected > view v2 > hide sel & #6.2-12,14-21#!6.1 atoms > show sel & #6.2-12,14-21#!6.1 surfaces > transparency sel 50 surfaces > select clear > lighting soft > transparency sel 90 surfaces > select #6 54421 atoms, 56148 bonds, 1975 pseudobonds, 6431 residues, 29 models selected > select subtract #6.13 53512 atoms, 55248 bonds, 1975 pseudobonds, 6298 residues, 49 models selected > transparency sel 90 surfaces > select clear > undo > color sel white surfaces > transparency sel 50 surfaces > select clear > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/Ec_S13.png > width 3000 height 2182 supersample 3 transparentBackground true > close sur Expected a models specifier or a keyword > hide #!6.1-21 surfaces > show #!5 models > hide #5.32,54#!5.1-31,33-53,55-63#!6.1-21 surfaces > ui tool show ""Side View"" > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/Ec_Tb_S13.png > width 3000 height 2182 supersample 3 transparentBackground true > view list Named views: side, v1, v2 > view side > show #!1 models > hide #!5 models > hide #!6 models > show #!6 models > hide #!6 models > show #!6 models > ribbon #6 > view side > cartoon style modeHelix tubes Invalid ""modeHelix"" argument: Should be one of 'default', 'tube', or 'wrap' > cartoon style modeHelix tube > view side Drag select of 127 residues > cartoon style modeHelix default > surface #1 > transparency #1 100 surfaces > ~ribbon #1 Drag select of mS37_A2 SES surface, 8905 of 200914 triangles, RNA_AA SES surface, 294190 of 3001286 triangles, bS6m_AE SES surface, 2561 of 190136 triangles, uS7m_AF SES surface, 16774 of 313164 triangles, uS11m_AI SES surface, 42527 of 186812 triangles, 192 residues > select clear Drag select of mS38_A3 SES surface, 1747 of 136332 triangles, RNA_AA SES surface, 98766 of 3001286 triangles, uS7m_AF SES surface, 265 of 313164 triangles, uS11m_AI SES surface, 794 of 186812 triangles, uS14m_AK SES surface, 11253 of 170088 triangles, mS31_AY SES surface, 3998 of 190180 triangles, 79 residues Drag select of RNA_AA SES surface, 3542 of 3001286 triangles, uS15m_AL SES surface, 1097 of 266718 triangles, 10 residues > select clear > ui mousemode right translate > transparency #1 80 surfaces > color #1 grey surfaces > color #1 grey white Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color #1 white surfaces > lighting simple > lighting soft > graphics silhouettes false > graphics silhouettes true > lighting flat > lighting soft > transparency #1 50 surfaces > view side > transparency #1 80 surfaces > transparency #1 75 surfaces > transparency #1 60 surfaces > transparency #1 30 surfaces > transparency #1 20 surfaces > lighting flat > lighting full > lighting soft > view side > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_Hs_surface_soft.png > width 3000 height 2182 supersample 3 transparentBackground true > lighting flat > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/SSU_side_Ec_Hs_surface_flat.png > width 3000 height 2182 supersample 3 transparentBackground true > lighting soft > view v1 > save > /Users/ondrejgahura/Work/Publications/MitoRiboProteins/Figures/Fig_S13/detail_Ec_Hs_soft_v2.png > width 3000 height 2182 supersample 3 transparentBackground true > hide #!1 models > show #!5 models > close session > open > /Users/ondrejgahura/Work/Publications/Bnonstop_editing/ChimeraX/RESC-A.cxs > format session opened ChimeraX session > view list Named views: default > view default > lighting soft > show #17 models > hide #17 models > open > /Users/ondrejgahura/Work/Publications/Bnonstop_editing/AF_metacentrum/download-Q04cDMVwqsg9pVGIzGKsxeVT8gKHGfwwpZcswgutER6GCodjdRTDCLknw2MRlboU.zip Unrecognized file suffix '.zip' > open > /Users/ondrejgahura/Work/Publications/Bnonstop_editing/AF_metacentrum/bnresc3corrected/relaxed_model_1_pred_0.pdb Chain information for relaxed_model_1_pred_0.pdb #18 --- Chain | Description A | No description available > hide #18 models > show #18 models > matchmaker #18 to #16 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 RESC3_corrected_meta_Colab, chain A (#16) with relaxed_model_1_pred_0.pdb, chain A (#18), sequence alignment score = 3455.9 RMSD between 419 pruned atom pairs is 0.761 angstroms; (across all 688 pairs: 9.150) > hide #16 models > show #16 models > select add #18 11132 atoms, 11223 bonds, 688 residues, 1 model selected > color bfactor sel 11132 atoms, 688 residues, atom bfactor range 27.9 to 94.3 > hide #16 models > show #16 models > undo > color sel yellow > rename #18 RESC3_Bn_corrected_AF_meta > hide #18 models > view default > save > /Users/ondrejgahura/Work/Publications/Bnonstop_editing/ChimeraX/RESC-A.cxs ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-18.7.4 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 645 OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,3 Processor Name: Quad-Core Intel Core i5 Processor Speed: 1,4 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 256 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.120.10.0.0 (iBridge: 19.16.15071.0.0,0) OS Loader Version: 540.120.3~6 Software: System Software Overview: System Version: macOS 12.4 (21F79) Kernel Version: Darwin 21.5.0 Time since boot: 6 days 6:45 Graphics/Displays: Intel Iris Plus Graphics 645: Chipset Model: Intel Iris Plus Graphics 645 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3ea6 Revision ID: 0x0001 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 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: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 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: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 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-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 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: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core fixed Tom Goddard all ChimeraX