id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 10215 Crash in garbage collection while fetching mmCIF haaris.safdari@… Greg Couch "{{{ The following bug report has been submitted: Platform: macOS-14.1.1-x86_64-i386-64bit ChimeraX Version: 1.7.dev202307312254 (2023-07-31 22:54:15 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x00007000139d1000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00007ff854ac4b40 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/plistlib.py"", line 174 in parse File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/plistlib.py"", line 875 in load File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/platform.py"", line 425 in _mac_ver_xml File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/platform.py"", line 448 in mac_ver File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/fetch.py"", line 332 in html_user_agent File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/fetch.py"", line 153 in retrieve_url File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/fetch.py"", line 88 in fetch_file File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py"", line 97 in fetch File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 454 in remember_data_format File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 483 in collated_open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 154 in provider_open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py"", line 119 in cmd_open File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2897 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 893 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1044 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, 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""SIRI_UNDERSTANDING_NL_OVERRIDES"" : ""654e391a4a6560536bdb1c80"" }, ""deploymentId"" : 240000529 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== > mousemode shift leftMode ""translate selected models"" > mousemode shift middleMode ""rotate selected models"" > mousemode rightMode zoom > mousemode control wheelMode ""contour level"" > mousemode setting ""contour level"" speed 0.1 > mousemode shift wheelMode ""rotate selected models"" > camera ortho > set bgColor grey > lighting shadows false > lighting depthCue false > graphics silhouettes true > lighting simple > functionkey F1 cofr sel > functionkey F2 mousemode rightMode 'mark surface' > functionkey F3 mousemode rightMode 'move markers' > functionkey F4 mk 3 1 > functionkey F5 view > functionkey F6 view sel pad 0.92 clip false > functionkey F7 mousemode rightMode 'delete markers' > functionkey F8 mousemode rightMode zoom > functionkey F9 sequence chain sel > functionkey F10 transparency sel 65 > functionkey F11 transparency sel 0 > functionkey F12 tool show 'Fit in Map' > color name f01graublau #BADBED Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed > color name f02silber #F6FAFC Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc > color name f03muschel #FFFFE5 Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5 > color name f04beige #F3F3A9 Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9 > color name f05gelb #f2b701 Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701 > color name f06orange #e68310 Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310 > color name f07rotorange #FF6A25 Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25 > color name f08rot #dd3d2d Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d > color name f09lachs #f97b72 Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72 > color name f10flieder #D57AD5 Color 'f10flieder' is opaque: 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f21anthrazit #323F45 Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45 > alias localres color sample #$1 map #$2 offset 0.1 update true palette > ""#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"" > range $3,$4 > alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1 > $2' > alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4 > 'quickmk $1 $2' > alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3 > alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep > $3 > alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep > $3 > alias consurf color byattr seq_conservation protein palette cyanmaroon > novalue yellow > alias chaininfo preset custom chaininfo > alias foto save browse format tiff height 4000 supersample 4 > transparentBackground false > alias durch save browse format tiff height 4000 supersample 4 > transparentBackground true > alias session save browse format session includeMaps true compress lz4 > alias nomapsession save browse format session includeMaps false compress lz4 > alias splitup color zone #$1 near sel sharpEdges true distance $2 > alias quicksplitup color zone #$1 near sel sharpEdges false distance $2 > alias spalt volume splitbyzone #$1 > alias undust surface undust #$1 > alias dust1 surface dust #$1 size 1 > alias dust2 surface dust #$1 size 2 > alias dust3 surface dust #$1 size 3 > alias dust4 surface dust #$1 size 4 > alias dust5 surface dust #$1 size 5 > alias dust6 surface dust #$1 size 6 > alias dust7 surface dust #$1 size 7 > alias dust8 surface dust #$1 size 8 > alias dust9 surface dust #$1 size 9 > alias dust10 surface dust #$1 size 10 > alias dust11 surface dust #$1 size 11 > alias dust12 surface dust #$1 size 12 > alias dust13 surface dust #$1 size 13 > alias dust14 surface dust #$1 size 14 > alias dust15 surface dust #$1 size 15 > alias dust20 surface dust #$1 size 20 > alias dust25 surface dust #$1 size 25 > alias dust30 surface dust #$1 size 30 > alias dust35 surface dust #$1 size 35 > alias dust40 surface dust #$1 size 40 > alias dust45 surface dust #$1 size 45 > alias dust50 surface dust #$1 size 50 > alias sunset color sample #$1 map #$2 offset 0.1 update true palette > ""#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"" > range $3,$4 > alias nicemap volume #$1 subdivideSurface true surfacesmoothing true > smoothLines true squareMesh false meshLighting true > alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false > smoothLines false squareMesh true meshLighting true > alias figure lighting soft ; lighting multishadow 1024 ; graphics > silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ; > camera ortho UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/Haaris/Desktop/Modelling_Ksg/postprocess_masked.mrc > /Users/Haaris/Desktop/Modelling_Ksg/run_class001.mrc Opened postprocess_masked.mrc as #1.1, grid size 400,400,400, pixel 0.832, shown at level 0.0108, step 2, values float32 Opened run_class001.mrc as #1.2, grid size 400,400,400, pixel 0.832, shown at level 0.00636, step 2, values float32 > open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot11.pdb Chain information for Haaris_Kasugamycin_Coot11.pdb #2 --- Chain | Description A | No description available D | No description available E | No description available F | No description available H | No description available K | No description available L | No description available O | No description available P | No description available Q | No description available R | No description available T | No description available U | No description available W | No description available X | No description available > show cartoons > hide atoms > set bgColor white > volume #1.2 step 1 > volume #1.1 step 1 > volume #1.2 level 0.008035 > hide #!1.1 models > volume #1.2 level 0.005687 > open /Users/Haaris/Desktop/Modelling_Ksg/J142_cluster_004.mrc Opened J142_cluster_004.mrc as #3, grid size 140,140,140, pixel 2.4, shown at level 0.948, step 1, values float32 > close #3 > open ""/Users/Haaris/Desktop/Modelling_Ksg/cryosparc_P18_J36_007_volume_map > (1).mrc"" Opened cryosparc_P18_J36_007_volume_map (1).mrc as #3, grid size 420,420,420, pixel 0.8, shown at level 0.0551, step 2, values float32 > volume #3 step 1 > select add #3 2 models selected > view matrix models > #3,-0.17708,-0.65534,0.73428,169.84,-0.85404,0.47311,0.21628,182.61,-0.48913,-0.58881,-0.64347,436.19 > view matrix models > #3,-0.17708,-0.65534,0.73428,172.46,-0.85404,0.47311,0.21628,197.46,-0.48913,-0.58881,-0.64347,451.55 > view matrix models > #3,-0.03201,-0.75958,0.64963,178.48,-0.89725,0.30821,0.31615,213.05,-0.44036,-0.57276,-0.69139,449.04 > view matrix models > #3,-0.03201,-0.75958,0.64963,184.48,-0.89725,0.30821,0.31615,214.97,-0.44036,-0.57276,-0.69139,451.36 Fit in map shortcut requires 1 displayed atomic model and 1 map or two maps, got 1 atomic models, 2 maps. > hide #!1.2 models > hide #!1 models > hide #!2 models > show #!1.2 models > fitmap #3 inMap #1.2 Fit map cryosparc_P18_J36_007_volume_map (1).mrc in map run_class001.mrc using 739407 points correlation = 0.9474, correlation about mean = 0.8298, overlap = 1512 steps = 276, shift = 6.9, angle = 16.1 degrees Position of cryosparc_P18_J36_007_volume_map (1).mrc (#3) relative to run_class001.mrc (#1.2) coordinates: Matrix rotation and translation 0.17069831 -0.69465086 0.69880060 130.53409619 -0.94857678 0.07602228 0.30728279 257.03875485 -0.26657867 -0.71531867 -0.64595279 440.20267930 Axis -0.71558737 0.67554491 -0.17769013 Axis point 0.00000000 319.54658078 128.79028775 Rotation angle (degrees) 134.39621182 Shift along axis 2.01300185 > hide #!1.2 models > select subtract #3 Nothing selected > show #!1.2 models > volume resample #3 onGrid #1.2 Opened cryosparc_P18_J36_007_volume_map (1).mrc resampled as #4, grid size 400,400,400, pixel 0.832, shown at step 1, values float32 > close #3 > save ""/Users/Haaris/Desktop/Modelling_Ksg/cryosparc_P18_J36_007_volume_map > (1).mrc"" models #4 > hide #!1.2 models > show #!1.2 models > hide #!4 models > show #!2 models > color #1.2 #b2b2b276 models > volume #4 level 0.07887 > volume #4 level 0.08536 > volume #4 level 0.06588 > volume #4 level 0.0464 > volume #1.2 level 0.006608 > volume #1.2 level 0.00845 > hide #!2 models > hide #!1.2 models > hide #!4 models > show #!2 models > show #!1.2 models > hide #!1.2 models > show #!1.2 models > hide #!1.2 models > open /Users/Haaris/Desktop/Modelling_Ksg/5lmn_aligned.pdb Chain information for 5lmn_aligned.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available V | No description available W | No description available X | No description available Y | No description available > close #3 > open /Users/Haaris/Desktop/Modelling_Ksg/5np6_aligned.pdb Chain information for 5np6_aligned.pdb #3 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 3 | No description available 4 | No description available A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available X | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available v | No description available w | No description available x | No description available y | No description available z | No description available > hide #!2 models > show #3 cartoons > hide #3 atoms > select #3/B:22 23 atoms, 25 bonds, 1 residue, 1 model selected > select up 1623 atoms, 1812 bonds, 76 residues, 1 model selected > select up 146883 atoms, 159526 bonds, 10662 residues, 1 model selected > select down 1623 atoms, 1812 bonds, 76 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #3/B Alignment identifier is 3/B > select #3/B:33 20 atoms, 21 bonds, 1 residue, 1 model selected > select #3/B:33 20 atoms, 21 bonds, 1 residue, 1 model selected > select #3/B:70 20 atoms, 21 bonds, 1 residue, 1 model selected > select #3/B:70 20 atoms, 21 bonds, 1 residue, 1 model selected > select #3/B:53 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:53 23 atoms, 25 bonds, 1 residue, 1 model selected > show #!2 models > hide #!2 models > select #3/B:24 23 atoms, 25 bonds, 1 residue, 1 model selected > select #3/B:24 23 atoms, 25 bonds, 1 residue, 1 model selected > hide #3 models > show #!1.2 models > open /Users/Haaris/Desktop/Modelling_Ksg/Haaris_Kasugamycin_Coot12.pdb Chain information for Haaris_Kasugamycin_Coot12.pdb #5 --- Chain | Description A | No description available B | No description available D | No description available E | No description available F | No description available H | No description available K | No description available L | No description available O | No description available P | No description available Q | No description available R | No description available T | No description available U | No description available W | No description available X | No description available > show #!5 cartoons > hide #!5 atoms > volume #1.2 level 0.004075 > volume #1.2 level 0.006493 > hide #!1 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > show #!4 models > hide #!4 models > select add #1.2 23 atoms, 25 bonds, 1 residue, 3 models selected > show #!1.1 models > hide #!1.1 models > show #!1.1 models > hide #!1.1 models > hide #!5 models > hide #!1.2 models > show #!5 models > hide #!5 models > show #!5 models > show #!4 models > hide #!4 models > show #!4 models > hide #!5 models > hide #!4 models > open 5lmo Summary of feedback from opening 5lmo fetched from pdb --- note | Fetching compressed mmCIF 5lmo from http://files.rcsb.org/download/5lmo.cif 5lmo title: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1B) [more info...] Chain information for 5lmo #6 --- Chain | Description | UniProt A | 16S rRNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Non-standard residues in 5lmo #6 --- A — adenosine-5'-monophosphate G — guanosine-5'-monophosphate MG — magnesium ion U — uridine-5'-monophosphate ZN — zinc ion > show #!6 cartoons > hide #!6 atoms > open 5lmp Summary of feedback from opening 5lmp fetched from pdb --- note | Fetching compressed mmCIF 5lmp from http://files.rcsb.org/download/5lmp.cif 5lmp title: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1C) [more info...] Chain information for 5lmp #7 --- Chain | Description | UniProt A | 16S rRNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Non-standard residues in 5lmp #7 --- MG — magnesium ion ZN — zinc ion > close #6 > select add #7 54155 atoms, 58316 bonds, 1819 pseudobonds, 4267 residues, 7 models selected > close #7 > close > open 5lmn 5lmn title: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1A) [more info...] Chain information for 5lmn #1 --- Chain | Description | UniProt A | 16S ribosomal RNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Non-standard residues in 5lmn #1 --- MG — magnesium ion ZN — zinc ion > open 5lmo 5lmo title: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1B) [more info...] Chain information for 5lmo #2 --- Chain | Description | UniProt A | 16S rRNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Non-standard residues in 5lmo #2 --- A — adenosine-5'-monophosphate G — guanosine-5'-monophosphate MG — magnesium ion U — uridine-5'-monophosphate ZN — zinc ion > open 5lmp 5lmp title: Structure of bacterial 30S-IF1-IF3-mRNA translation pre-initiation complex (state-1C) [more info...] Chain information for 5lmp #3 --- Chain | Description | UniProt A | 16S rRNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Non-standard residues in 5lmp #3 --- MG — magnesium ion ZN — zinc ion > open 5lmq Summary of feedback from opening 5lmq fetched from pdb --- note | Fetching compressed mmCIF 5lmq from http://files.rcsb.org/download/5lmq.cif 5lmq title: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex, open form (state-2A) [more info...] Chain information for 5lmq #4 --- Chain | Description | UniProt A | 16S rRNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Z | tRNA | Non-standard residues in 5lmq #4 --- MG — magnesium ion ZN — zinc ion > open 5lmr Summary of feedback from opening 5lmr fetched from pdb --- note | Fetching compressed mmCIF 5lmr from http://files.rcsb.org/download/5lmr.cif 5lmr title: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2B) [more info...] Chain information for 5lmr #5 --- Chain | Description | UniProt A | 16S rRNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Z | tRNAi | Non-standard residues in 5lmr #5 --- MG — magnesium ion ZN — zinc ion > open 5lms Summary of feedback from opening 5lms fetched from pdb --- note | Fetching compressed mmCIF 5lms from http://files.rcsb.org/download/5lms.cif 5lms title: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-2C) [more info...] Chain information for 5lms #6 --- Chain | Description | UniProt A | 16S rRNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Z | tRNAi | Non-standard residues in 5lms #6 --- MG — magnesium ion ZN — zinc ion > open 5lmt Summary of feedback from opening 5lmt fetched from pdb --- note | Fetching compressed mmCIF 5lmt from http://files.rcsb.org/download/5lmt.cif 5lmt title: Structure of bacterial 30S-IF1-IF3-mRNA-tRNA translation pre-initiation complex(state-3) [more info...] Chain information for 5lmt #7 --- Chain | Description | UniProt A | 16S ribosomal RNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 W | Translation initiation factor IF-1 | IF1_THET8 0-71 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Z | tRNAi | Non-standard residues in 5lmt #7 --- MG — magnesium ion ZN — zinc ion > open 5lmu Summary of feedback from opening 5lmu fetched from pdb --- note | Fetching compressed mmCIF 5lmu from http://files.rcsb.org/download/5lmu.cif 5lmu title: Structure of bacterial 30S-IF3-mRNA-tRNA translation pre-initiation complex, closed form (state-4) [more info...] Chain information for 5lmu #8 --- Chain | Description | UniProt A | 16S ribosomal RNA | B | 30S ribosomal protein S2 | RS2_THET8 1-256 C | 30S ribosomal protein S3 | RS3_THET8 1-239 D | 30S ribosomal protein S4 | RS4_THET8 1-209 E | 30S ribosomal protein S5 | RS5_THET8 1-162 F | 30S ribosomal protein S6 | RS6_THET8 1-101 G | 30S ribosomal protein S7 | RS7_THET8 1-156 H | 30S ribosomal protein S8 | RS8_THET8 1-138 I | 30S ribosomal protein S9 | RS9_THET8 1-128 J | 30S ribosomal protein S10 | RS10_THET8 1-105 K | 30S ribosomal protein S11 | RS11_THET8 1-129 L | 30S ribosomal protein S12 | RS12_THET8 4-135 M | 30S ribosomal protein S13 | RS13_THET8 1-126 N | 30S ribosomal protein S14 type Z | RS14Z_THET8 1-61 O | 30S ribosomal protein S15 | RS15_THET8 1-89 P | 30S ribosomal protein S16 | RS16_THET8 1-88 Q | 30S ribosomal protein S17 | RS17_THET8 1-105 R | 30S ribosomal protein S18 | RS18_THET8 1-88 S | 30S ribosomal protein S19 | RS19_THET8 1-93 T | 30S ribosomal protein S20 | RS20_THET8 1-106 V | 30S ribosomal protein Thx | RSHX_THET8 1-27 X | Translation initiation factor IF-3 | IF3_THET8 2-172 Y | mRNA | Z | tRNAi | Non-standard residues in 5lmu #8 --- MG — magnesium ion ZN — zinc ion > open 5lmv ===== Log before crash end ===== Log: > mousemode shift leftMode ""translate selected models"" > mousemode shift middleMode ""rotate selected models"" > mousemode rightMode zoom > mousemode control wheelMode ""contour level"" > mousemode setting ""contour level"" speed 0.1 > mousemode shift wheelMode ""rotate selected models"" > camera ortho > set bgColor grey > lighting shadows false > lighting depthCue false > graphics silhouettes true > lighting simple > functionkey F1 cofr sel > functionkey F2 mousemode rightMode 'mark surface' > functionkey F3 mousemode rightMode 'move markers' > functionkey F4 mk 3 1 > functionkey F5 view > functionkey F6 view sel pad 0.92 clip false > functionkey F7 mousemode rightMode 'delete markers' > functionkey F8 mousemode rightMode zoom > functionkey F9 sequence chain sel > functionkey F10 transparency sel 65 > functionkey F11 transparency sel 0 > functionkey F12 tool show 'Fit in Map' > color name f01graublau #BADBED Color 'f01graublau' is opaque: rgb(72.9%, 85.9%, 92.9%) hex: #badbed > color name f02silber #F6FAFC Color 'f02silber' is opaque: rgb(96.5%, 98%, 98.8%) hex: #f6fafc > color name f03muschel #FFFFE5 Color 'f03muschel' is opaque: rgb(100%, 100%, 89.8%) hex: #ffffe5 > color name f04beige #F3F3A9 Color 'f04beige' is opaque: rgb(95.3%, 95.3%, 66.3%) hex: #f3f3a9 > color name f05gelb #f2b701 Color 'f05gelb' is opaque: rgb(94.9%, 71.8%, 0.392%) hex: #f2b701 > color name f06orange #e68310 Color 'f06orange' is opaque: rgb(90.2%, 51.4%, 6.27%) hex: #e68310 > color name f07rotorange #FF6A25 Color 'f07rotorange' is opaque: rgb(100%, 41.6%, 14.5%) hex: #ff6a25 > color name f08rot #dd3d2d Color 'f08rot' is opaque: rgb(86.7%, 23.9%, 17.6%) hex: #dd3d2d > color name f09lachs #f97b72 Color 'f09lachs' is opaque: rgb(97.6%, 48.2%, 44.7%) hex: #f97b72 > color name f10flieder #D57AD5 Color 'f10flieder' is opaque: rgb(83.5%, 47.8%, 83.5%) hex: #d57ad5 > color name f11violett #cf1c90 Color 'f11violett' is opaque: rgb(81.2%, 11%, 56.5%) hex: #cf1c90 > color name f12lila #4b148f Color 'f12lila' is opaque: rgb(29.4%, 7.84%, 56.1%) hex: #4b148f > color name f13dunkelblau #2E2EF7 Color 'f13dunkelblau' is opaque: rgb(18%, 18%, 96.9%) hex: #2e2ef7 > color name f14blau #00AAFF Color 'f14blau' is opaque: rgb(0%, 66.7%, 100%) hex: #00aaff > color name f15cyan #60e2d6 Color 'f15cyan' is opaque: rgb(37.6%, 88.6%, 83.9%) hex: #60e2d6 > color name f16blaugrün #30ffa6 Color 'f16blaugrün' is opaque: rgb(18.8%, 100%, 65.1%) hex: #30ffa6 > color name f17grün #00FF00 Color 'f17grün' is opaque: rgb(0%, 100%, 0%) hex: #00ff00 > color name f18dunkelgrün #228B22 Color 'f18dunkelgrün' is opaque: rgb(13.3%, 54.5%, 13.3%) hex: #228b22 > color name f19hellgrau #DCDCDC Color 'f19hellgrau' is opaque: gray(86.3%) hex: #dcdcdc > color name f20grau #B2B2B2 Color 'f20grau' is opaque: gray(69.8%) hex: #b2b2b2 > color name f21anthrazit #323F45 Color 'f21anthrazit' is opaque: rgb(19.6%, 24.7%, 27.1%) hex: #323f45 > alias localres color sample #$1 map #$2 offset 0.1 update true palette > ""#0000E7:#001CE7:#0039E7:#0056E7:#0073E7:#0090E7:#00ADE7:#00CAE7:#00E7E7:#00E7CA:#00E7AD:#00E790:#00E773:#00E756:#00E739:#00E71C:#00E700:#1CE700:#39E700:#56E700:#73E700:#90E700:#ADE700:#CAE700:#E7E700:#E7CA00:#E7AD00:#E79000:#E77300:#E75600:#E73900:#E71C00:#E70000"" > range $3,$4 > alias mk color zone #$2 near #$1 sharpEdges true distance 3; fun F4 'mk $1 > $2' > alias quickmk color zone #$2 near #$1 sharpEdges false distance 3; fun F4 > 'quickmk $1 $2' > alias mapcolour color zone #$2 near #$1 sharpEdges true distance $3 > alias mapmorph volume morph #$1 #$2 constantVolume true frames 9999 playStep > $3 > alias mapseries volume morph #$1-$2 constantVolume true frames 9999 playStep > $3 > alias consurf color byattr seq_conservation protein palette cyanmaroon > novalue yellow > alias chaininfo preset custom chaininfo > alias foto save browse format tiff height 4000 supersample 4 > transparentBackground false > alias durch save browse format tiff height 4000 supersample 4 > transparentBackground true > alias session save browse format session includeMaps true compress lz4 > alias nomapsession save browse format session includeMaps false compress lz4 > alias splitup color zone #$1 near sel sharpEdges true distance $2 > alias quicksplitup color zone #$1 near sel sharpEdges false distance $2 > alias spalt volume splitbyzone #$1 > alias undust surface undust #$1 > alias dust1 surface dust #$1 size 1 > alias dust2 surface dust #$1 size 2 > alias dust3 surface dust #$1 size 3 > alias dust4 surface dust #$1 size 4 > alias dust5 surface dust #$1 size 5 > alias dust6 surface dust #$1 size 6 > alias dust7 surface dust #$1 size 7 > alias dust8 surface dust #$1 size 8 > alias dust9 surface dust #$1 size 9 > alias dust10 surface dust #$1 size 10 > alias dust11 surface dust #$1 size 11 > alias dust12 surface dust #$1 size 12 > alias dust13 surface dust #$1 size 13 > alias dust14 surface dust #$1 size 14 > alias dust15 surface dust #$1 size 15 > alias dust20 surface dust #$1 size 20 > alias dust25 surface dust #$1 size 25 > alias dust30 surface dust #$1 size 30 > alias dust35 surface dust #$1 size 35 > alias dust40 surface dust #$1 size 40 > alias dust45 surface dust #$1 size 45 > alias dust50 surface dust #$1 size 50 > alias sunset color sample #$1 map #$2 offset 0.1 update true palette > ""#364B9A:#4A7BB7:#6EA6CD:#98CAE1:#C2E4EF:#EAECCC:#FEDA8B:#FDB366:#F67E4B:#DD3D2D:#A50026"" > range $3,$4 > alias nicemap volume #$1 subdivideSurface true surfacesmoothing true > smoothLines true squareMesh false meshLighting true > alias unnicemap volume #$1 subdivideSurface false surfacesmoothing false > smoothLines false squareMesh true meshLighting true > alias figure lighting soft ; lighting multishadow 1024 ; graphics > silhouettes true color black width $1 depthJump 0.03 ; set bgColor white ; > camera ortho UCSF ChimeraX version: 1.7.dev202307312254 (2023-07-31) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-5.1.35 OpenGL renderer: AMD Radeon Pro 580X OpenGL Engine OpenGL vendor: ATI Technologies 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: iMac Model Identifier: iMac19,1 Processor Name: 6-Core Intel Core i5 Processor Speed: 3,7 GHz Number of Processors: 1 Total Number of Cores: 6 L2 Cache (per Core): 256 KB L3 Cache: 9 MB Memory: 32 GB System Firmware Version: 2020.40.3.0.0 OS Loader Version: 580~743 SMC Version (system): 2.46f13 Software: System Software Overview: System Version: macOS 14.1.1 (23B81) Kernel Version: Darwin 23.1.0 Time since boot: 3 days, 2 hours, 39 minutes Graphics/Displays: Radeon Pro 580X: Chipset Model: Radeon Pro 580X Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x67df Revision ID: 0x00c0 ROM Revision: 113-D0008A-042 VBIOS Version: 113-D0008A1X-009 EFI Driver Version: 01.B1.042 Metal Support: Metal 2 Displays: iMac: Display Type: Built-In Retina LCD Resolution: Retina 5K (5120 x 2880) Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2412M: Resolution: 1920 x 1200 (WUXGA - Widescreen Ultra eXtended Graphics Array) UI Looks like: 1920 x 1200 Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 0FFXD31242JL Mirror: Off Online: Yes Rotation: Supported Connection Type: Thunderbolt/DisplayPort Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.2.1 Babel: 2.12.1 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: 1.6.2 charset-normalizer: 3.2.0 ChimeraX-AddCharge: 1.5.11 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.9.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.46.1 ChimeraX-AtomicLibrary: 10.0.8 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: 2.10.4 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: 1.0.2 ChimeraX-CheckWaters: 1.3.1 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.3 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.dev202307312254 ChimeraX-CoreFormats: 1.1 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: 1.1.2 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: 1.2.1 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 ChimeraX-Log: 1.1.5 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.2 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: 2.1.1 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 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.9 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0 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: 1.10.2 ChimeraX-PDB: 2.7.2 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.2 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: 1.1.1 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: 3.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.1 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.9 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.1 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.1 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-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: 1.31.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.2.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.1 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.1.3 contourpy: 1.1.0 cxservices: 1.2.2 cycler: 0.11.0 Cython: 0.29.33 debugpy: 1.6.7 decorator: 5.1.1 docutils: 0.19 executing: 1.2.0 filelock: 3.9.0 fonttools: 4.41.1 funcparserlib: 1.0.1 grako: 3.16.5 h5py: 3.9.0 html2text: 2020.1.16 idna: 3.4 ihm: 0.38 imagecodecs: 2023.7.10 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.0 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.3.1 jupyterlab-widgets: 3.0.8 kiwisolver: 1.4.4 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: 1.5.7 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.4 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 10.0.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 3.10.0 prompt-toolkit: 3.0.39 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: 2.14.0 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 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 pyzmq: 25.1.0 qtconsole: 5.4.3 QtPy: 2.3.1 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: 2.4.1 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.4 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.1 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 stack-data: 0.6.2 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.3.2 traitlets: 5.9.0 typing-extensions: 4.7.1 tzdata: 2023.3 urllib3: 2.0.4 wcwidth: 0.2.6 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.8 }}} " defect closed normal Core can't reproduce chimerax-programmers all ChimeraX