id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15477 Crash in Qt event loop in io_connect_method(), Intel Mac ChimeraX running on Mac M1 Tzu-Jing.Yang@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-13.0.1-x86_64-i386-64bit ChimeraX Version: 1.8 (2024-06-10 23:15:52 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x00000002003732c0 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, psutil._psutil_osx, psutil._psutil_posix, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, 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""\/Applications\/ChimeraX-1.8.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.11\/lib\/python3.11\/site-packages\/numpy\/.dylibs\/libopenblas64_.0.dylib"", ""name"" : ""libopenblas64_.0.dylib"" } ], ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000413 }, { ""rolloutId"" : ""61fd92db295c182621ececc3"", ""factorPackIds"" : { }, ""deploymentId"" : 240000387 } ], ""experiments"" : [ { ""treatmentId"" : ""c47ab4cc-c9c3-4b5d-a87c-e2433ce02597"", ""experimentId"" : ""6639bc6ba73d460582162323"", ""deploymentId"" : 400000006 }, { ""treatmentId"" : ""3dff9c91-a8fb-424e-a656-c8d6e6037574"", ""experimentId"" : ""662152ede2d11d1408c4db33"", ""deploymentId"" : 400000014 } ] }, ""reportNotes"" : [ ""dyld_process_snapshot_create_for_process failed with 5"" ] } ===== Log before crash start ===== Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > open /Users/tjyang/Downloads/cryosparc_P34_J14_class_04_01600_volume.mrc Opened cryosparc_P34_J14_class_04_01600_volume.mrc as #1, grid size 128,128,128, pixel 4.18, shown at level 3.38, step 1, values float32 > set bgColor white > lighting soft > close > open /Users/tjyang/Downloads/cryosparc_P34_J16_001_volume_map(1).mrc Opened cryosparc_P34_J16_001_volume_map(1).mrc as #1, grid size 160,160,160, pixel 3.35, shown at level 2.55, step 1, values float32 > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting soft Mismatch between Cocoa '\x0' and Carbon '\u3112' for virtual key 9 with QFlags(NoModifier) Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with QFlags(ShiftModifier) Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with QFlags(ControlModifier) Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with QFlags(ShiftModifier|ControlModifier) Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with QFlags(AltModifier) Mismatch between Cocoa '\x0' and Carbon 'V' for virtual key 9 with QFlags(ShiftModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with QFlags(ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon 'v' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|AltModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ShiftModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ShiftModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ControlModifier|AltModifier|MetaModifier) Mismatch between Cocoa '\x0' and Carbon '\x16' for virtual key 9 with QFlags(ShiftModifier|ControlModifier|AltModifier|MetaModifier) > volume flip #1 Opened cryosparc_P34_J16_001_volume_map(1).mrc z flip as #2, grid size 160,160,160, pixel 3.35, shown at step 1, values float32 > close #1 > ui mousemode right zoom > volume #2 level 1.837 > volume #2 level 2.628 > volume #2 level 0.2734 > ui tool show ""Side View"" > volume #2 level 1.506 > volume #2 level 0.4206 > volume #2 level 0.1998 > volume #2 level 0.3838 > hide #!2 models > show #!2 models > volume #2 level 0.6229 > volume #2 level 0.9908 > open /Users/tjyang/Downloads/cryosparc_P34_J14_class_04_02000_volume.mrc Opened cryosparc_P34_J14_class_04_02000_volume.mrc as #1, grid size 128,128,128, pixel 4.18, shown at level 3.35, step 1, values float32 > hide #!2 models > volume #1 level 1.449 > volume #1 level 1.72 > volume #1 level 1.942 > close #1 > open /Users/tjyang/Downloads/cryosparc_P34_J14_class_02_02000_volume.mrc Opened cryosparc_P34_J14_class_02_02000_volume.mrc as #1, grid size 128,128,128, pixel 4.18, shown at level 3.37, step 1, values float32 > volume #1 level 1.847 > close #1 > close #2 > open 7tut Summary of feedback from opening 7tut fetched from pdb --- warnings | Atom HO5' is not in the residue template for G /q:1 Atom HO5' is not in the residue template for G /u:1 Atom HO5' is not in the residue template for C /v:1 7tut title: Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon [more info...] Chain information for 7tut #1 --- Chain | Description | UniProt 1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476 2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96 3 | Protein transport protein Sec61 gamma | 4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483 5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106 6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224 7 | Nicalin | A0A8C0S144_CANLF -41-521 8 | Calcium load-activated calcium channel | 9 | Obligate partner of TMCO1 insertase | A | uL2 | G1TT27_RABIT 1-257 B | Nascent chain | C | uL4 | G1SVW5_RABIT 1-413 D | uL18 | G1SYJ6_RABIT 1-297 E | eL6 | G1SKF7_RABIT 1-291 F | uL30 | G1TUB1_RABIT 1-247 G | eL8 | G1STW0_RABIT 1-319 H | uL6 | G1SWI6_RABIT 1-192 I | uL16 | B7NZQ2_RABIT 1-214 J | uL5 | G1TUB8_RABIT 1-178 K | 28S ribosomal RNA | L | eL13 | G1TPV0_RABIT 1-211 M | eL14 | G1SZ12_RABIT 1-218 N | eL15 | G1T0C1_RABIT 0-204 O | uL13 | P | uL22 | G1TVT6_RABIT 1-184 Q | eL18 | R | eL19 | G1TJR3_RABIT 1-196 S | eL20 | T | eL21 | G1SHQ2_RABIT 1-160 U | eL22 | G1TSG1_RABIT 1-128 V | uL14 | G1T6D1_RABIT 1-140 W | eL24 | G1SE28_RABIT 1-157 X | eL23 | G1SE76_RABIT 1-156 Y | uL24 | G1SQH0_RABIT 1-145 Z | eL27 | G1TXF6_RABIT 1-136 a | uL15 | G1SNY0_RABIT 1-148 b | eL29 | G1SGR6_RABIT 1-226 c | eL30 | G1TDL2_RABIT 1-115 d | eL31 | G1SHG0_RABIT 1-125 e | eL32 | G1U437_RABIT 1-135 f | eL33 | G1SF08_RABIT 1-110 g | eL34 | G1U945_RABIT 1-116 h | eL35 | G1SIT5_RABIT 1-123 i | eL36 | G1TTQ5_RABIT 1-105 j | eL37 | U3KPD5_RABIT 1-97 k | eL38 | G1U001_RABIT 1-70 l | eL39 | G1TTN1_RABIT 1-51 m | eL40 | A0A2K5PSA0_CEBIM 10-102 n | eL41 | A0A087WNH4_RABIT 1-25 o | eL42 | G1U344_RABIT 1-106 p | eL43 | G1SY53_RABIT 1-92 q | P-site tRNA | r | eL28 | G1U7L1_RABIT 1-137 u | 5S ribosomal RNA | v | 5.8S ribosomal RNA | w | uL3 | G1TL06_RABIT 2-403 Non-standard residues in 7tut #1 --- MG — magnesium ion ZN — zinc ion > close #1 > open emdb:21435 Opened emdb 21435 as #1, grid size 500,500,500, pixel 1.36, shown at level 0.0073, step 2, values float32, fit PDB 6w6l The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 step 1 > volume #1 level 0.008496 > open 6w6l Summary of feedback from opening 6w6l fetched from pdb --- warning | Atom H1 is not in the residue template for UNK /y:1 6w6l title: Cryo-EM structure of the human ribosome-TMCO1 translocon [more info...] Chain information for 6w6l #2 --- Chain | Description | UniProt 1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_HUMAN 1-476 2 | Protein transport protein Sec61 subunit gamma | SC61G_HUMAN 1-68 3 | Protein transport protein Sec61 subunit beta | SC61B_HUMAN 1-96 4 | Transmembrane protein 147 | TM147_HUMAN 1-224 5 | Nicalin | NCLN_HUMAN 1-563 6 | Calcium load-activated calcium channel | TMCO1_HUMAN 1-188 7 | Coiled-coil domain-containing protein 47 | CCD47_HUMAN 1-483 A | 60S ribosomal protein L8 | RL8_HUMAN 1-257 B | 60S ribosomal protein L3 | RL3_HUMAN 1-403 C | 60S ribosomal protein L4 | RL4_HUMAN 1-427 D | 5.8S ribosomal RNA | E | 5S ribosomal RNA | F | 60S ribosomal protein L5 | RL5_HUMAN 1-297 G | 60S ribosomal protein L6 | RL6_HUMAN 1-288 H | 60S ribosomal protein L7 | RL7_HUMAN 1-248 I | 60S ribosomal protein L7a | RL7A_HUMAN 1-266 J | 60S ribosomal protein L9 | RL9_HUMAN 1-192 K | 60S ribosomal protein L10 | RL10_HUMAN 1-214 L | 60S ribosomal protein L11 | RL11_HUMAN 1-178 M | 60S ribosomal protein L13 | RL13_HUMAN 1-211 N | 60S ribosomal protein L14 | RL14_HUMAN 1-215 O | 60S ribosomal protein L15 | RL15_HUMAN 1-204 P | 60S ribosomal protein L13a | RL13A_HUMAN 1-203 Q | 60S ribosomal protein L17 | RL17_HUMAN 1-184 R | 60S ribosomal protein L18 | RL18_HUMAN 1-188 S | 60S ribosomal protein L19 | RL19_HUMAN 1-196 T | 60S ribosomal protein L18a | RL18A_HUMAN 1-176 U | 60S ribosomal protein L21 | RL21_HUMAN 1-160 V | 60S ribosomal protein L22 | RL22_HUMAN 1-128 W | 60S ribosomal protein L23 | X | 60S ribosomal protein L24 | RL24_HUMAN 1-157 Y | 60S ribosomal protein L23a | RL23A_HUMAN 1-156 Z | 60S ribosomal protein L26 | RL26_HUMAN 1-145 a | 60S ribosomal protein L27 | RL27_HUMAN 1-136 b | 60S ribosomal protein L27a | RL27A_HUMAN 1-148 c | 60S ribosomal protein L29 | RL29_HUMAN 1-159 d | 60S ribosomal protein L30 | RL30_HUMAN 1-115 e | 60S ribosomal protein L31 | f | 60S ribosomal protein L32 | RL32_HUMAN 1-135 g | 60S ribosomal protein L35a | RL35A_HUMAN 1-110 h | 60S ribosomal protein L34 | RL34_HUMAN 1-117 i | 60S ribosomal protein L35 | RL35_HUMAN 1-123 j | 60S ribosomal protein L36 | RL36_HUMAN 1-105 k | 60S ribosomal protein L37 | RL37_HUMAN 1-97 l | 60S ribosomal protein L38 | RL38_HUMAN 1-70 m | 60S ribosomal protein L39 | RL39_HUMAN 1-51 o | 60S ribosomal protein L41 | RL41_HUMAN 1-25 p | 60S ribosomal protein L36a | J3KQN4_HUMAN 1-106 q | 60S ribosomal protein L37a | RL37A_HUMAN 1-92 r | 60S ribosomal protein L28 | RL28_HUMAN 1-137 t | 28S ribosomal RNA | u | tRNA | v | tRNA | y | Nascent chain mixture | Non-standard residues in 6w6l #2 --- MG — magnesium ion ZN — zinc ion > select #2 259082 atoms, 270245 bonds, 3798 pseudobonds, 11953 residues, 4 models selected > hide sel atoms > show sel cartoons > volume #1 color #b2b2b280 > select clear > close #1-2 > open EMDB:26133 Opened emdb 26133 as #1, grid size 412,412,412, pixel 1.34, shown at level 0.5, step 2, values float32, fit PDB 7tut The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > volume #1 step 1 > volume #1 level 0.6564 > open 7tut Summary of feedback from opening 7tut fetched from pdb --- warnings | Atom HO5' is not in the residue template for G /q:1 Atom HO5' is not in the residue template for G /u:1 Atom HO5' is not in the residue template for C /v:1 7tut title: Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon [more info...] Chain information for 7tut #2 --- Chain | Description | UniProt 1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476 2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96 3 | Protein transport protein Sec61 gamma | 4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483 5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106 6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224 7 | Nicalin | A0A8C0S144_CANLF -41-521 8 | Calcium load-activated calcium channel | 9 | Obligate partner of TMCO1 insertase | A | uL2 | G1TT27_RABIT 1-257 B | Nascent chain | C | uL4 | G1SVW5_RABIT 1-413 D | uL18 | G1SYJ6_RABIT 1-297 E | eL6 | G1SKF7_RABIT 1-291 F | uL30 | G1TUB1_RABIT 1-247 G | eL8 | G1STW0_RABIT 1-319 H | uL6 | G1SWI6_RABIT 1-192 I | uL16 | B7NZQ2_RABIT 1-214 J | uL5 | G1TUB8_RABIT 1-178 K | 28S ribosomal RNA | L | eL13 | G1TPV0_RABIT 1-211 M | eL14 | G1SZ12_RABIT 1-218 N | eL15 | G1T0C1_RABIT 0-204 O | uL13 | P | uL22 | G1TVT6_RABIT 1-184 Q | eL18 | R | eL19 | G1TJR3_RABIT 1-196 S | eL20 | T | eL21 | G1SHQ2_RABIT 1-160 U | eL22 | G1TSG1_RABIT 1-128 V | uL14 | G1T6D1_RABIT 1-140 W | eL24 | G1SE28_RABIT 1-157 X | eL23 | G1SE76_RABIT 1-156 Y | uL24 | G1SQH0_RABIT 1-145 Z | eL27 | G1TXF6_RABIT 1-136 a | uL15 | G1SNY0_RABIT 1-148 b | eL29 | G1SGR6_RABIT 1-226 c | eL30 | G1TDL2_RABIT 1-115 d | eL31 | G1SHG0_RABIT 1-125 e | eL32 | G1U437_RABIT 1-135 f | eL33 | G1SF08_RABIT 1-110 g | eL34 | G1U945_RABIT 1-116 h | eL35 | G1SIT5_RABIT 1-123 i | eL36 | G1TTQ5_RABIT 1-105 j | eL37 | U3KPD5_RABIT 1-97 k | eL38 | G1U001_RABIT 1-70 l | eL39 | G1TTN1_RABIT 1-51 m | eL40 | A0A2K5PSA0_CEBIM 10-102 n | eL41 | A0A087WNH4_RABIT 1-25 o | eL42 | G1U344_RABIT 1-106 p | eL43 | G1SY53_RABIT 1-92 q | P-site tRNA | r | eL28 | G1U7L1_RABIT 1-137 u | 5S ribosomal RNA | v | 5.8S ribosomal RNA | w | uL3 | G1TL06_RABIT 2-403 Non-standard residues in 7tut #2 --- MG — magnesium ion ZN — zinc ion > select #2 267107 atoms, 278108 bonds, 4182 pseudobonds, 12662 residues, 4 models selected > hide sel atoms > select #2/1-9 32434 atoms, 32776 bonds, 2025 residues, 1 model selected > show sel cartoons > select clear > volume #1 level 0.5 > volume #1 level 0.6642 > volume #1 color #b2b2b280 > open /Users/tjyang/Downloads/cryosparc_P34_J16_001_volume_map(1).mrc Opened cryosparc_P34_J16_001_volume_map(1).mrc as #3, grid size 160,160,160, pixel 3.35, shown at level 2.55, step 1, values float32 > volume flip #3 Opened cryosparc_P34_J16_001_volume_map(1).mrc z flip as #4, grid size 160,160,160, pixel 3.35, shown at step 1, values float32 > close #3 > select add #4 2 models selected > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models #4,1,0,0,78.459,0,1,0,-176.31,0,0,1,-57.318 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.88842,-0.3649,-0.27851,279.31,0.42165,0.88853,0.18088,-302.77,0.18146,-0.27814,0.94325,-14.059 > view matrix models > #4,0.64154,-0.67449,-0.36537,452.33,0.23706,-0.27867,0.93067,-119.88,-0.72954,-0.68368,-0.01888,582.26 > view matrix models > #4,0.67226,-0.51404,-0.53275,442,0.28693,-0.48246,0.82759,-50.663,-0.68245,-0.70922,-0.17684,616.71 > view matrix models > #4,0.63939,-0.4983,-0.58556,459.67,0.38622,-0.45037,0.80498,-80.142,-0.66484,-0.74085,-0.09551,600.29 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.63939,-0.4983,-0.58556,388.44,0.38622,-0.45037,0.80498,103.47,-0.66484,-0.74085,-0.09551,666.09 > fitmap #4 inMap #1 Fit map cryosparc_P34_J16_001_volume_map(1).mrc z flip in map emdb 26133 using 40940 points correlation = 0.9562, correlation about mean = 0.5321, overlap = 1.915e+05 steps = 272, shift = 17, angle = 28.1 degrees Position of cryosparc_P34_J16_001_volume_map(1).mrc z flip (#4) relative to emdb 26133 (#1) coordinates: Matrix rotation and translation 0.27976532 -0.70296789 -0.65388648 559.71623510 0.20902266 -0.62014713 0.75612637 194.78282853 -0.93703837 -0.34821502 -0.02655944 628.25264255 Axis -0.75642098 0.19394549 0.62466987 Axis point 0.00000000 347.99237503 489.79100520 Rotation angle (degrees) 133.11544864 Shift along axis 6.84663922 > select clear > ui mousemode right translate > ui mousemode right zoom > volume #4 level 0.15 > volume #4 level 0.4995 > hide #!4 models > show #!4 models > hide #!1 models > hide #!2 models > volume #4 level 0.1132 > hide #!4 models > show #!1 models > show #!2 models > volume #1 level 0.6642 > hide #!1 models > hide #!2 models > show #!4 models > volume #4 level 0.4075 > volume #4 level 0.3708 > hide #!4 models > show #!1 models > volume #1 color #b2b2b2 > lighting soft > volume #1 level 0.5391 > hide #!1 models > show #!4 models > open > /Users/tjyang/Downloads/cryosparc_P34_J15_class_01_00020_volume_sharp.mrc Opened cryosparc_P34_J15_class_01_00020_volume_sharp.mrc as #3, grid size 128,128,128, pixel 4.18, shown at level 3.33, step 1, values float32 > hide #!4 models > volume #3 level 0.6787 > volume #3 level 0.569 > volume #3 level 0.1849 > volume #3 level 0.4958 > volume #3 level 0.3312 > volume #3 level 1.685 > open /Users/tjyang/Downloads/cryosparc_P34_J16_002_volume_map.mrc Opened cryosparc_P34_J16_002_volume_map.mrc as #5, grid size 160,160,160, pixel 3.35, shown at level 2.54, step 1, values float32 > hide #!3 models > volume #5 level 0.4151 > volume #5 level 0.6172 > volume #5 level 0.5364 > volume #5 level 0.2534 > open /Users/tjyang/Downloads/cryosparc_P34_J16_002_volume_map_sharp.mrc Opened cryosparc_P34_J16_002_volume_map_sharp.mrc as #6, grid size 160,160,160, pixel 3.35, shown at level 3.03, step 1, values float32 > hide #!5 models > volume #6 level 0.4088 > volume #6 level 0.6953 > hide #!6 models > show #!5 models > volume #5 level 0.3949 > hide #!5 models > show #!6 models > volume #6 level 0.5521 > volume #6 level 0.6953 > open /Users/tjyang/Downloads/fold_2024_05_14_09_26_model_0.cif Chain information for fold_2024_05_14_09_26_model_0.cif #7 --- Chain | Description A | . B | . C | . D | . > select add #7 7189 atoms, 7354 bonds, 915 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,233.09,0,1,0,362.25,0,0,1,182.83 > ui mousemode right zoom > ui mousemode right ""translate selected models"" > view matrix models #7,1,0,0,296.27,0,1,0,350.43,0,0,1,124.89 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.73677,-0.48572,0.47036,290.77,0.32436,-0.35646,-0.8762,360.44,0.59326,0.79813,-0.10508,137.77 > select #7 7189 atoms, 7354 bonds, 915 residues, 1 model selected > hide sel cartoons > select #7/B 1465 atoms, 1492 bonds, 191 residues, 1 model selected > show sel cartoons > color #7 bychain > color #6 darkgrey > select clear > select add #7 7189 atoms, 7354 bonds, 915 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #7,0.73677,-0.48572,0.47036,282.26,0.32436,-0.35646,-0.8762,353.41,0.59326,0.79813,-0.10508,115.88 > view matrix models > #7,0.73677,-0.48572,0.47036,277.99,0.32436,-0.35646,-0.8762,342.22,0.59326,0.79813,-0.10508,108.8 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.73954,0.63264,-0.22988,280.18,0.18776,-0.52186,-0.83211,339.61,-0.64639,0.57222,-0.50472,87.538 > view matrix models > #7,-0.33485,0.65229,-0.67999,262.51,0.29331,-0.61364,-0.73308,341.15,-0.89546,-0.44492,0.01415,81.289 > view matrix models > #7,-0.74518,-0.46224,-0.48067,249.96,0.65203,-0.35384,-0.67057,348.43,0.13988,-0.8131,0.56507,96.524 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.74518,-0.46224,-0.48067,271.56,0.65203,-0.35384,-0.67057,355.08,0.13988,-0.8131,0.56507,157.81 > view matrix models > #7,-0.74518,-0.46224,-0.48067,263.19,0.65203,-0.35384,-0.67057,353.75,0.13988,-0.8131,0.56507,161.88 > ui mousemode right ""rotate selected models"" > view matrix models > #7,-0.8109,-0.54881,-0.20312,264.69,0.45439,-0.37179,-0.80951,349.7,0.36875,-0.74872,0.55086,165.04 > view matrix models > #7,-0.80042,-0.56023,-0.21321,264.6,0.47903,-0.38399,-0.78936,350.11,0.36035,-0.73396,0.57572,165.34 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.80042,-0.56023,-0.21321,265.35,0.47903,-0.38399,-0.78936,350.28,0.36035,-0.73396,0.57572,164.14 > select #6 2 models selected > view matrix models #6,1,0,0,0.070482,0,1,0,1.7356,0,0,1,0.38287 > select clear > ui mousemode right zoom > volume #6 color #a9a9a980 > select #7 7189 atoms, 7354 bonds, 915 residues, 1 model selected > select #7/C 3578 atoms, 3657 bonds, 447 residues, 1 model selected > show sel cartoons > select #6 2 models selected > select clear > volume #6 color darkgrey > volume #6 level 0.4088 > volume #6 color #a9a9a980 > ui mousemode right translate > ui mousemode right zoom > volume #6 level 0.5998 > volume #6 level 0.6953 > show #!2 models > hide #!2 models > volume #6 level 0.9818 > show #!2 models > show #!1 models > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > volume #6 color darkgrey > select add #6 2 models selected > select add #7 7189 atoms, 7354 bonds, 915 residues, 3 models selected > ui mousemode right ""translate selected models"" > select add #5 7189 atoms, 7354 bonds, 915 residues, 5 models selected > close #4 > view matrix models > #5,1,0,0,139.39,0,1,0,-121.58,0,0,1,-150.74,#6,1,0,0,139.46,0,1,0,-119.84,0,0,1,-150.36,#7,-0.80042,-0.56023,-0.21321,404.74,0.47903,-0.38399,-0.78936,228.7,0.36035,-0.73396,0.57572,13.393 > ui mousemode right ""rotate selected models"" > view matrix models > #5,0.89136,-0.31226,0.32858,167.49,0.4524,0.65818,-0.60177,22.649,-0.028355,0.68505,0.72795,-261.26,#6,0.89136,-0.31226,0.32858,167.14,0.4524,0.65818,-0.60177,23.593,-0.028355,0.68505,0.72795,-259.8,#7,-0.74465,-0.62063,0.2456,348.57,-0.26368,-0.064511,-0.96245,274.47,0.61317,-0.78145,-0.11561,90.653 > view matrix models > #5,-0.16048,0.38857,-0.90734,550.78,-0.35913,0.83326,0.42036,-92.921,0.91939,0.39331,0.0058216,-223.97,#6,-0.16048,0.38857,-0.90734,551.09,-0.35913,0.83326,0.42036,-91.339,0.91939,0.39331,0.0058216,-223.22,#7,-0.012371,0.60665,-0.79487,495.37,0.83809,-0.42729,-0.33915,172.65,-0.54539,-0.67037,-0.50314,158.71 > ui mousemode right ""translate selected models"" > view matrix models > #5,-0.16048,0.38857,-0.90734,440.11,-0.35913,0.83326,0.42036,37.267,0.91939,0.39331,0.0058216,-57.319,#6,-0.16048,0.38857,-0.90734,440.43,-0.35913,0.83326,0.42036,38.849,0.91939,0.39331,0.0058216,-56.569,#7,-0.012371,0.60665,-0.79487,384.71,0.83809,-0.42729,-0.33915,302.84,-0.54539,-0.67037,-0.50314,325.36 > fitmap #6 inMap #1 Fit map cryosparc_P34_J16_002_volume_map_sharp.mrc in map emdb 26133 using 92194 points correlation = 0.8977, correlation about mean = 0.6195, overlap = 3.379e+05 steps = 308, shift = 25.9, angle = 24.2 degrees Position of cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) relative to emdb 26133 (#1) coordinates: Matrix rotation and translation -0.32718154 0.67956357 -0.65661679 354.91883527 -0.24172322 0.61155440 0.75337316 -16.49084666 0.91352183 0.40520932 -0.03582302 -66.70997287 Axis -0.18784511 -0.84713812 -0.49706259 Axis point 209.67292814 0.00000000 111.13661725 Rotation angle (degrees) 112.06913452 Shift along axis -19.54071241 > select clear > hide #!2 models > hide #!1 models > ui mousemode right zoom > volume #6 level 0.7908 > select add #7 7189 atoms, 7354 bonds, 915 residues, 1 model selected > volume #6 level 0.6476 > ui mousemode right ""translate selected models"" > view matrix models > #7,-0.012371,0.60665,-0.79487,395.9,0.83809,-0.42729,-0.33915,254.19,-0.54539,-0.67037,-0.50314,320.97 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.40154,0.27505,-0.87356,391.04,0.83556,-0.50055,0.22646,256.75,-0.37498,-0.82085,-0.43081,319.44 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.40154,0.27505,-0.87356,398.97,0.83556,-0.50055,0.22646,258.47,-0.37498,-0.82085,-0.43081,316.75 > view matrix models > #7,0.40154,0.27505,-0.87356,398.56,0.83556,-0.50055,0.22646,262.52,-0.37498,-0.82085,-0.43081,318.93 > view matrix models > #7,0.40154,0.27505,-0.87356,399.24,0.83556,-0.50055,0.22646,262.49,-0.37498,-0.82085,-0.43081,316.33 > ui mousemode right ""rotate selected models"" > view matrix models > #7,0.48809,0.28494,-0.82497,398.54,0.76515,-0.59443,0.24739,263.3,-0.41989,-0.75198,-0.50815,316.48 > view matrix models > #7,0.47706,0.25411,-0.84133,398.57,0.75248,-0.6127,0.24161,263.4,-0.45409,-0.74834,-0.48351,316.96 > ui mousemode right ""translate selected models"" > view matrix models > #7,0.47706,0.25411,-0.84133,398.71,0.75248,-0.6127,0.24161,262.68,-0.45409,-0.74834,-0.48351,312.26 > view matrix models > #7,0.47706,0.25411,-0.84133,399.12,0.75248,-0.6127,0.24161,260.89,-0.45409,-0.74834,-0.48351,313.55 > select clear > ui mousemode right ""rotate selected models"" > select clear > volume #6 level 0.8863 > hide #7 models > volume #6 level 0.743 > show #7 models > volume #6 level 0.7 > volume #6 level 0.6 > volume #6 color #a9a9a980 > ui mousemode right zoom > show #!2 models > select #2 267107 atoms, 278108 bonds, 4182 pseudobonds, 12662 residues, 4 models selected > hide sel cartoons > log chains #2 Chain information for 7tut #2 --- Chain | Description | UniProt 1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476 2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96 3 | Protein transport protein Sec61 gamma | 4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483 5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106 6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224 7 | Nicalin | A0A8C0S144_CANLF -41-521 8 | Calcium load-activated calcium channel | 9 | Obligate partner of TMCO1 insertase | A | uL2 | G1TT27_RABIT 1-257 B | Nascent chain | C | uL4 | G1SVW5_RABIT 1-413 D | uL18 | G1SYJ6_RABIT 1-297 E | eL6 | G1SKF7_RABIT 1-291 F | uL30 | G1TUB1_RABIT 1-247 G | eL8 | G1STW0_RABIT 1-319 H | uL6 | G1SWI6_RABIT 1-192 I | uL16 | B7NZQ2_RABIT 1-214 J | uL5 | G1TUB8_RABIT 1-178 K | 28S ribosomal RNA | L | eL13 | G1TPV0_RABIT 1-211 M | eL14 | G1SZ12_RABIT 1-218 N | eL15 | G1T0C1_RABIT 0-204 O | uL13 | P | uL22 | G1TVT6_RABIT 1-184 Q | eL18 | R | eL19 | G1TJR3_RABIT 1-196 S | eL20 | T | eL21 | G1SHQ2_RABIT 1-160 U | eL22 | G1TSG1_RABIT 1-128 V | uL14 | G1T6D1_RABIT 1-140 W | eL24 | G1SE28_RABIT 1-157 X | eL23 | G1SE76_RABIT 1-156 Y | uL24 | G1SQH0_RABIT 1-145 Z | eL27 | G1TXF6_RABIT 1-136 a | uL15 | G1SNY0_RABIT 1-148 b | eL29 | G1SGR6_RABIT 1-226 c | eL30 | G1TDL2_RABIT 1-115 d | eL31 | G1SHG0_RABIT 1-125 e | eL32 | G1U437_RABIT 1-135 f | eL33 | G1SF08_RABIT 1-110 g | eL34 | G1U945_RABIT 1-116 h | eL35 | G1SIT5_RABIT 1-123 i | eL36 | G1TTQ5_RABIT 1-105 j | eL37 | U3KPD5_RABIT 1-97 k | eL38 | G1U001_RABIT 1-70 l | eL39 | G1TTN1_RABIT 1-51 m | eL40 | A0A2K5PSA0_CEBIM 10-102 n | eL41 | A0A087WNH4_RABIT 1-25 o | eL42 | G1U344_RABIT 1-106 p | eL43 | G1SY53_RABIT 1-92 q | P-site tRNA | r | eL28 | G1U7L1_RABIT 1-137 u | 5S ribosomal RNA | v | 5.8S ribosomal RNA | w | uL3 | G1TL06_RABIT 2-403 > select #2/1-3 8915 atoms, 9011 bonds, 562 residues, 1 model selected > show sel cartoons > select clear > volume #6 level 0.4568 > open 7tut Summary of feedback from opening 7tut fetched from pdb --- warnings | Atom HO5' is not in the residue template for G /q:1 Atom HO5' is not in the residue template for G /u:1 Atom HO5' is not in the residue template for C /v:1 7tut title: Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon [more info...] Chain information for 7tut #4 --- Chain | Description | UniProt 1 | Protein transport protein Sec61 subunit alpha isoform 1 | S61A1_CANLF 1-476 2 | Protein transport protein Sec61 subunit beta | SC61B_CANLF 1-96 3 | Protein transport protein Sec61 gamma | 4 | Coiled-coil domain containing 47 | A0A8C0RJF2_CANLF 1-483 5 | PAT complex subunit Asterix | A0A8C0TSD6_CANLF 1-106 6 | Transmembrane protein 147 | A0A8C0RUW0_CANLF 1-224 7 | Nicalin | A0A8C0S144_CANLF -41-521 8 | Calcium load-activated calcium channel | 9 | Obligate partner of TMCO1 insertase | A | uL2 | G1TT27_RABIT 1-257 B | Nascent chain | C | uL4 | G1SVW5_RABIT 1-413 D | uL18 | G1SYJ6_RABIT 1-297 E | eL6 | G1SKF7_RABIT 1-291 F | uL30 | G1TUB1_RABIT 1-247 G | eL8 | G1STW0_RABIT 1-319 H | uL6 | G1SWI6_RABIT 1-192 I | uL16 | B7NZQ2_RABIT 1-214 J | uL5 | G1TUB8_RABIT 1-178 K | 28S ribosomal RNA | L | eL13 | G1TPV0_RABIT 1-211 M | eL14 | G1SZ12_RABIT 1-218 N | eL15 | G1T0C1_RABIT 0-204 O | uL13 | P | uL22 | G1TVT6_RABIT 1-184 Q | eL18 | R | eL19 | G1TJR3_RABIT 1-196 S | eL20 | T | eL21 | G1SHQ2_RABIT 1-160 U | eL22 | G1TSG1_RABIT 1-128 V | uL14 | G1T6D1_RABIT 1-140 W | eL24 | G1SE28_RABIT 1-157 X | eL23 | G1SE76_RABIT 1-156 Y | uL24 | G1SQH0_RABIT 1-145 Z | eL27 | G1TXF6_RABIT 1-136 a | uL15 | G1SNY0_RABIT 1-148 b | eL29 | G1SGR6_RABIT 1-226 c | eL30 | G1TDL2_RABIT 1-115 d | eL31 | G1SHG0_RABIT 1-125 e | eL32 | G1U437_RABIT 1-135 f | eL33 | G1SF08_RABIT 1-110 g | eL34 | G1U945_RABIT 1-116 h | eL35 | G1SIT5_RABIT 1-123 i | eL36 | G1TTQ5_RABIT 1-105 j | eL37 | U3KPD5_RABIT 1-97 k | eL38 | G1U001_RABIT 1-70 l | eL39 | G1TTN1_RABIT 1-51 m | eL40 | A0A2K5PSA0_CEBIM 10-102 n | eL41 | A0A087WNH4_RABIT 1-25 o | eL42 | G1U344_RABIT 1-106 p | eL43 | G1SY53_RABIT 1-92 q | P-site tRNA | r | eL28 | G1U7L1_RABIT 1-137 u | 5S ribosomal RNA | v | 5.8S ribosomal RNA | w | uL3 | G1TL06_RABIT 2-403 Non-standard residues in 7tut #4 --- MG — magnesium ion ZN — zinc ion > select #4 267107 atoms, 278108 bonds, 4182 pseudobonds, 12662 residues, 4 models selected > hide sel atoms > show sel cartoons > hide sel cartoons > select #4/1-3 8915 atoms, 9011 bonds, 562 residues, 1 model selected > show sel cartoons > volume #6 level 0.791 > fitmap sel inMap #6 Fit molecule 7tut (#4) to map cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) using 8915 atoms average map value = 0.8183, steps = 48 shifted from previous position = 2.05 rotated from previous position = 2.92 degrees atoms outside contour = 4446, contour level = 0.79098 Position of 7tut (#4) relative to cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.35193617 -0.27357238 0.89515311 196.51973488 0.64800324 0.61889748 0.44391181 -206.52902182 -0.67545001 0.73629074 -0.04053662 256.09912553 Axis 0.15852788 0.85158114 0.49967838 Axis point 220.74112503 0.00000000 110.87713924 Rotation angle (degrees) 112.75476506 Shift along axis -16.75516713 > select clear > hide #!2 models > volume #6 level 0.1703 > volume #6 level 0.5523 > select #7/B 1465 atoms, 1492 bonds, 191 residues, 1 model selected > select #7/B,C 5043 atoms, 5149 bonds, 638 residues, 1 model selected > volume #6 level 0.6477 > volume #6 level 0.6 > open /Users/tjyang/Downloads/fold_2024_05_14_09_26_model_0.cif Chain information for fold_2024_05_14_09_26_model_0.cif #8 --- Chain | Description A | . B | . C | . D | . > mmaker #8 to #7 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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score = 2307.5 RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs: 0.000) > color #8 bychain > select clear > hide #7 models > select #8/B,C 5043 atoms, 5149 bonds, 638 residues, 1 model selected > fitmap sel inMap #6 Fit molecule fold_2024_05_14_09_26_model_0.cif (#8) to map cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) using 5043 atoms average map value = 1.705, steps = 108 shifted from previous position = 34.3 rotated from previous position = 17.2 degrees atoms outside contour = 1990, contour level = 0.6 Position of fold_2024_05_14_09_26_model_0.cif (#8) relative to cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.90815609 -0.38320038 -0.16855258 280.53093727 0.40222756 -0.68711436 -0.60505109 332.61942350 0.11604091 -0.61727733 0.77814085 187.17954519 Axis -0.01463366 -0.34063150 0.94008299 Axis point 100.67849424 232.97883767 0.00000000 Rotation angle (degrees) 155.30776538 Shift along axis 58.55846017 > mmaker #8 to #7 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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score = 2307.5 RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs: 0.000) > select #8/C inmap #6 Expected a keyword > fitmap #8/C inMap #6 Fit molecule fold_2024_05_14_09_26_model_0.cif (#8) to map cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) using 3578 atoms average map value = 1.842, steps = 116 shifted from previous position = 39.5 rotated from previous position = 21.2 degrees atoms outside contour = 1291, contour level = 0.6 Position of fold_2024_05_14_09_26_model_0.cif (#8) relative to cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation -0.91152941 -0.30352026 -0.27746997 287.30065986 0.41123301 -0.67480759 -0.61279859 333.11986580 -0.00124206 -0.67268875 0.73992451 189.77891996 Axis -0.07792012 -0.35938644 0.92993002 Axis point 114.48319125 234.38713212 0.00000000 Rotation angle (degrees) 157.39940731 Shift along axis 34.37585205 > select up 7189 atoms, 7354 bonds, 915 residues, 1 model selected > mmaker #8 to #7 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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score = 2307.5 RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs: 0.000) > select clear > hide #8 models > show #7 models > show #8 models > hide #7 models > show #!2 models > hide #!2 models > show #!2 models > select #2/1-9 32434 atoms, 32776 bonds, 2025 residues, 1 model selected > show sel cartoons > select clear > hide #8 models > show #8 models > hide #!6 models > hide #!2 models > show #7 models > hide #8 models > show #!1 models > hide #!1 models > show #!6 models > volume #6 level 0.6477 > volume #6 color darkgrey > hide #7 models > hide #!6 models > show #!5 models > hide #!4 models > show #!4 models > show #!6 models > fitmap #5 inMap #6 Fit map cryosparc_P34_J16_002_volume_map.mrc in map cryosparc_P34_J16_002_volume_map_sharp.mrc using 138645 points correlation = 0.9414, correlation about mean = 0.9112, overlap = 1.012e+06 steps = 136, shift = 26.1, angle = 24.2 degrees Position of cryosparc_P34_J16_002_volume_map.mrc (#5) relative to cryosparc_P34_J16_002_volume_map_sharp.mrc (#6) coordinates: Matrix rotation and translation 1.00000000 -0.00001533 -0.00004860 0.00529735 0.00001533 1.00000000 0.00009606 -0.01009414 0.00004860 -0.00009606 0.99999999 0.03937849 Axis -0.88339006 -0.44693405 0.14096791 Axis point 0.00000000 402.03719382 80.05834663 Rotation angle (degrees) 0.00623025 Shift along axis 0.00538289 > select clear > color #5 darkgrey > select clear > hide #!6 models > volume #5 level 0.4757 > volume #5 color #a9a9a9b3 > show #7 models > hide #!5 models > show #!6 models > hide #!6 models > show #!5 models > volume #6 level 1.125 > volume #5 level 0.496 > volume #5 level -0.009439 > volume #5 level 0.1523 > volume #5 level 0.4353 > show #8 models > hide #7 models > hide #8 models > show #8 models > hide #8 models > show #7 models > hide #!5 models > show #!5 models > show #8 models > hide #!5 models > hide #7 models > show #7 models > hide #7 models > hide #!4 models > select #8/C:!-70 Expected an objects specifier or a keyword > select #8/C:1-70 534 atoms, 552 bonds, 70 residues, 1 model selected > hide sel cartoons > select #8/C 3578 atoms, 3657 bonds, 447 residues, 1 model selected > ~select #8:1-100 2805 atoms, 2860 bonds, 347 residues, 1 model selected > show #!5 models > select #8/C 3578 atoms, 3657 bonds, 447 residues, 1 model selected > ~select #8:1-90 2883 atoms, 2939 bonds, 357 residues, 1 model selected > fitmap sel inMap #5 Fit molecule fold_2024_05_14_09_26_model_0.cif (#8) to map cryosparc_P34_J16_002_volume_map.mrc (#5) using 2883 atoms average map value = 2.225, steps = 228 shifted from previous position = 50.3 rotated from previous position = 40 degrees atoms outside contour = 410, contour level = 0.43531 Position of fold_2024_05_14_09_26_model_0.cif (#8) relative to cryosparc_P34_J16_002_volume_map.mrc (#5) coordinates: Matrix rotation and translation -0.55284171 -0.29334825 -0.77994413 288.88397895 0.83227870 -0.24040056 -0.49951949 316.13686704 -0.04096584 -0.92528610 0.37705095 208.66884110 Axis -0.30148467 -0.52326937 0.79705468 Axis point 113.62069640 294.74026807 0.00000000 Rotation angle (degrees) 135.08018356 Shift along axis -86.19835353 > mmaker #8 to #7 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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score = 2307.5 RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs: 0.000) > select #8/B,C 5043 atoms, 5149 bonds, 638 residues, 1 model selected > ~select #8:1-90 3654 atoms, 3724 bonds, 458 residues, 1 model selected > fitmap sel inMap #5 Fit molecule fold_2024_05_14_09_26_model_0.cif (#8) to map cryosparc_P34_J16_002_volume_map.mrc (#5) using 3654 atoms average map value = 2.101, steps = 148 shifted from previous position = 48 rotated from previous position = 27.9 degrees atoms outside contour = 557, contour level = 0.43531 Position of fold_2024_05_14_09_26_model_0.cif (#8) relative to cryosparc_P34_J16_002_volume_map.mrc (#5) coordinates: Matrix rotation and translation -0.68968697 -0.37002774 -0.62242377 290.11865428 0.71292906 -0.49745267 -0.49423980 324.30529604 -0.12674393 -0.78461475 0.60689015 198.58842110 Axis -0.23686827 -0.40434213 0.88340300 Axis point 110.74671265 262.70425652 0.00000000 Rotation angle (degrees) 142.19717065 Shift along axis -24.41658984 > mmaker #8 to #7 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 fold_2024_05_14_09_26_model_0.cif, chain C (#7) with fold_2024_05_14_09_26_model_0.cif, chain C (#8), sequence alignment score = 2307.5 RMSD between 447 pruned atom pairs is 0.000 angstroms; (across all 447 pairs: 0.000) > volume #5 level 0.6375 > volume #5 level 0.3342 > volume #5 level 0.3949 > select clear > hide #8 models > show #7 models > volume #6 level 1.364 > volume #6 level 0.6955 > hide #7 models > volume #6 level 0.6 > volume #6 level 0.5 > hide #!6 models > show #!5 models > volume #5 color darkgrey > volume #5 level 0.3342 > volume #5 level 0.2331 > volume #5 level 0.314 > volume #6 level 0.8342 > movie record > turn y 2 180 > wait 180 > movie encode /Users/tjyang/Desktop/movie21.mp4 Movie saved to /Users/tjyang/Desktop/movie21.mp4 > volume #6 level 1.121 > volume #5 level 0.6375 > volume #5 level 0.5364 ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.8 (2024-06-10) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 83 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: Z11D000L9D/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 8419.41.10 OS Loader Version: 8419.41.10 Software: System Software Overview: System Version: macOS 13.0.1 (22A400) Kernel Version: Darwin 22.1.0 Time since boot: 2 days, 3 hours, 19 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.15.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.7 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.57.1 ChimeraX-AtomicLibrary: 14.0.6 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.6 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.7 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.3 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.4 ChimeraX-DiffPlot: 1.0 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.10 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.2 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.0.3 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.5 ChimeraX-PDB: 2.7.5 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.1 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.4.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.0.15 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11.2 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.16.5 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.39.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.3 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.1 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.4 fonttools: 4.53.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.11.0 html2text: 2024.2.26 idna: 3.7 ihm: 1.0 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.3 jedi: 0.19.1 jinja2: 3.1.4 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.11 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.2.1 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.4 matplotlib-inline: 0.1.7 msgpack: 1.0.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.3.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.2 prompt-toolkit: 3.0.47 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.1.2 pyproject-hooks: 1.1.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.3 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.3 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 26.0.3 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.13.0 setuptools: 69.5.1 setuptools-scm: 8.0.4 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 7.2.6 sphinx-autodoc-typehints: 2.0.1 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.2 typing-extensions: 4.12.2 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.11 }}} " defect closed normal Volume Data can't reproduce all ChimeraX