id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 19740 Crash drawing widget while processing QGraphicsScene event chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.7.3-arm64-arm-64bit ChimeraX Version: 1.11 (2025-12-17 06:45:39 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Thread 0x0000000338497000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000033748b000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000033647f000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 948 in wait File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000335473000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000334467000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000033345b000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000033244f000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000331443000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x0000000330437000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000032f42b000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000032e41f000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000032d413000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Thread 0x000000032c407000 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 982 in run File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1045 in _bootstrap_inner File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1002 in _bootstrap Current thread 0x00000002066e2240 (most recent call first): File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 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, psutil._psutil_osx, psutil._psutil_posix, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, chimerax.map._map, 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Guard 56.0M 1 VM_ALLOCATE 365.0M 240 VM_ALLOCATE (reserved) 192.0M 2 reserved VM address space (unallocated) __AUTH 5438K 690 __AUTH_CONST 76.5M 937 __CTF 824 1 __DATA 33.2M 1064 __DATA_CONST 53.4M 1082 __DATA_DIRTY 2776K 341 __FONT_DATA 2352 1 __GLSLBUILTINS 5174K 1 __INFO_FILTER 8 1 __LINKEDIT 648.5M 139 __OBJC_RO 61.4M 1 __OBJC_RW 2397K 1 __TEXT 1.3G 1098 __TEXT (graphics) 1856K 4 __TPRO_CONST 128K 2 dyld private memory 1584K 15 mapped file 278.3M 55 page table in kernel 5895K 1 shared memory 3712K 27 =========== ======= ======= TOTAL 13.3G 6150 TOTAL, minus reserved VM space 13.2G 6150 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""b47fd867adeca91ca73bbe66ae8c22a2c121f60f"", ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""670ea6eb7a111748a97092a4"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""68db21af3b3ace402427b77b"" }, ""deploymentId"" : 240000189 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. > open ""/Users/zhangj14/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/081125_yeast_ribosomes_WT_P51_v3_zoom_S12.cxs"" Opened cryosparc_P51_J40_map_sharp.mrc as #5, grid size 700,700,700, pixel 0.93, shown at level 0.0457, step 1, values float32 Opened cryosparc_P51_J67_003_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 0.93, shown at level 0.478, step 2, values float32 Log from Mon Aug 11 01:17:32 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zhangj14/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"" Opened cryosparc_P51_J40_map_sharp.mrc as #5, grid size 700,700,700, pixel 0.93, shown at level 0.0968, step 1, values float32 Log from Sun Aug 10 00:06:22 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zhangj14/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"" Opened cryosparc_P51_J28_003_volume_map_sharp.mrc as #1, grid size 300,300,300, pixel 1.55, shown at level 1.28, step 1, values float32 Opened cryosparc_P51_J30_004_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 1.55, shown at level 0.769, step 1, values float32 Opened cryosparc_P51_J40_map_sharp.mrc as #5, grid size 700,700,700, pixel 0.93, shown at level 0.0935, step 1, values float32 Log from Fri Aug 8 16:22:56 2025UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/zhangj14 (Deleted)/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v1.cxs"" Opened cryosparc_P51_J28_003_volume_map_sharp.mrc as #1, grid size 300,300,300, pixel 1.55, shown at level 1.28, step 1, values float32 Opened cryosparc_P51_J30_004_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 1.55, shown at level 0.769, step 1, values float32 Log from Thu Aug 7 18:58:25 2025 Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/zhangj14 > (Deleted)/Downloads/cryosparc_P51_J28_003_volume_map_sharp.mrc"" Opened cryosparc_P51_J28_003_volume_map_sharp.mrc as #1, grid size 300,300,300, pixel 1.55, shown at level 0.793, step 2, values float32 > volume #1 step 1 > volume #1 level 1.576 > volume #1 level 1.523 > ui tool show ""Side View"" > open ""/Users/zhangj14 (Deleted)/Downloads/7top.cif"" 7top.cif title: Yeast 80S ribosome bound with the ALS/FTD-associated dipeptide repeat protein PR20 [more info...] Chain information for 7top.cif #2 --- Chain | Description | UniProt A25S | 25S rRNA | A58S | 5.8S rRNA | A5S | 5S rRNA | AL02 | 60S ribosomal protein L2-A | RL2A_YEAST 1-254 AL03 | RPL3 isoform 1 | A0A6A5Q627_YEASX 1-387 AL04 | RPL4A isoform 1 | A0A6A5Q3W0_YEASX 1-362 AL05 | RPL5 isoform 1 | A0A6A5Q0W8_YEASX 1-297 AL06 | 60S ribosomal protein L6-A | RL6A_YEAST 1-176 AL07 | 60S ribosomal protein L7-A | RL7A_YEAST 1-244 AL08 | 60S ribosomal protein L8-A | RL8A_YEAST 1-256 AL09 | 60S ribosomal protein L9-A | RL9A_YEAST 1-191 AL10 | RPL10 isoform 1 | A0A6A5PUZ5_YEASX 1-221 AL11 | RPL11A isoform 1 | A0A6A5Q7I9_YEASX 1-174 AL12 | Ribosomal protein L12 | AL13 | 60S ribosomal protein L13-A | RL13A_YEAST 1-199 AL14 | 60S ribosomal protein L14-A | RL14A_YEAST 1-138 AL15 | 60S ribosomal protein L15-A | RL15A_YEAST 1-204 AL16 | 60S ribosomal protein L16-A | RL16A_YEAST 1-199 AL17 | 60S ribosomal protein L17-A | RL17A_YEAST 1-184 AL18 | 60S ribosomal protein L18-A | RL18A_YEAST 1-186 AL19 | 60S ribosomal protein L19-A | RL19A_YEAST 1-189 AL20 | 60S ribosomal protein L20-A | RL20A_YEAST 1-172 AL21 | 60S ribosomal protein L21-A | RL21A_YEAST 1-160 AL22 | 60S ribosomal protein L22-A | RL22A_YEAST 1-121 AL23 | 60S ribosomal protein L23-A | RL23A_YEAST 1-137 AL24 | RPL24A isoform 1 | A0A6A5PY83_YEASX 1-155 AL25 | 60S ribosomal protein L25 | RL25_YEAST 1-142 AL26 | 60S ribosomal protein L26-A | RL26A_YEAST 1-127 AL27 | 60S ribosomal protein L27-A | RL27A_YEAST 1-136 AL28 | 60S ribosomal protein L28 | RL28_YEAST 1-149 AL29 | RPL29 isoform 1 | A0A6A5PWR1_YEASX 1-59 AL30 | 60S ribosomal protein L30 | RL30_YEAST 1-105 AL31 | 60S ribosomal protein L31-A | RL31A_YEAST 1-113 AL32 | RPL32 isoform 1 | A0A6A5Q1M9_YEASX 1-130 AL33 | 60S ribosomal protein L33-A | RL33A_YEAST 1-107 AL34 | 60S ribosomal protein L34-A | RL34A_YEAST 1-121 AL35 | 60S ribosomal protein L35-A | RL35A_YEAST 1-120 AL36 | 60S ribosomal protein L36-A | RL36A_YEAST 1-100 AL37 | 60S ribosomal protein L37-A | RL37A_YEAST 1-88 AL38 | RPL38 isoform 1 | A0A6A5PUL8_YEASX 1-78 AL39 | 60S ribosomal protein L39 | RL39_YEAST 1-51 AL40 | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 1-128 AL41 | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 AL42 | 60S ribosomal protein L42-A | RL44A_YEAST 1-106 AL43 | 60S ribosomal protein L43-A | RL43A_YEAST 1-92 ALP0 | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-198 APTN | tRNAfMet | PR | PR20 | A7H9Z6_ANADF 5-44 Non-standard residues in 7top.cif #2 --- ZN — zinc ion > show cartoons > hide atoms > select /AL03:226 11 atoms, 11 bonds, 1 residue, 1 model selected > select add #2 125433 atoms, 135363 bonds, 3255 pseudobonds, 9795 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,37.339,0,1,0,-7.8652,0,0,1,43.794 > view matrix models #2,1,0,0,15.226,0,1,0,28.613,0,0,1,32.277 > fitmap #2 inMap #1 Fit molecule 7top.cif (#2) to map cryosparc_P51_J28_003_volume_map_sharp.mrc (#1) using 125433 atoms average map value = 0.3492, steps = 144 shifted from previous position = 6.27 rotated from previous position = 8.68 degrees atoms outside contour = 116214, contour level = 1.5227 Position of 7top.cif (#2) relative to cryosparc_P51_J28_003_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.99089020 0.13452979 -0.00619227 -13.88799278 -0.13378894 0.98860761 0.06896025 45.34920950 0.01539893 -0.06750357 0.99760019 49.26567799 Axis -0.45216577 -0.07154131 -0.88906015 Axis point 295.00396215 260.22396537 0.00000000 Rotation angle (degrees) 8.67909868 Shift along axis -40.76481803 > view matrix models > #2,0.99089,0.13453,-0.0061923,-14.5,-0.13379,0.98861,0.06896,44.693,0.015399,-0.067504,0.9976,48.99 > view matrix models > #2,0.99089,0.13453,-0.0061923,-104.83,-0.13379,0.98861,0.06896,-64.35,0.015399,-0.067504,0.9976,46.95 > volume #1 level 2.638 > volume #1 level 1.735 > view matrix models > #2,0.99089,0.13453,-0.0061923,-146.61,-0.13379,0.98861,0.06896,-76.123,0.015399,-0.067504,0.9976,31.446 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.81638,0.57313,0.070995,-215.55,-0.33548,0.57071,-0.74949,209.85,-0.47008,0.58806,0.65819,62.897 > view matrix models > #2,0.78972,0.61345,-0.005138,-203.53,-0.42589,0.5422,-0.72431,229.35,-0.44154,0.57419,0.68945,53.803 > view matrix models > #2,0.53241,0.77534,-0.33969,-118.83,-0.68121,0.15423,-0.71565,359.47,-0.50249,0.61242,0.61029,73.874 > view > view matrix models > #2,0.017747,0.86222,-0.50622,1.3917,-0.91747,-0.1872,-0.35101,406.98,-0.39741,0.47067,0.78774,46.829 > view matrix models > #2,0.89579,0.40774,0.17693,-218.59,-0.15365,0.6576,-0.73753,152.42,-0.41707,0.63349,0.65173,43.978 > view matrix models > #2,0.92345,0.28201,0.2602,-214.72,-0.019791,0.71222,-0.70167,106.8,-0.3832,0.64281,0.66329,32.869 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.92345,0.28201,0.2602,-127.47,-0.019791,0.71222,-0.70167,238.57,-0.3832,0.64281,0.66329,55.488 > view matrix models > #2,0.92345,0.28201,0.2602,-88.009,-0.019791,0.71222,-0.70167,210.27,-0.3832,0.64281,0.66329,33.026 > view matrix models > #2,0.92345,0.28201,0.2602,-64.258,-0.019791,0.71222,-0.70167,222.79,-0.3832,0.64281,0.66329,42.61 > view matrix models > #2,0.92345,0.28201,0.2602,-64.446,-0.019791,0.71222,-0.70167,217,-0.3832,0.64281,0.66329,38.565 > fitmap #2 inMap #1 Fit molecule 7top.cif (#2) to map cryosparc_P51_J28_003_volume_map_sharp.mrc (#1) using 125433 atoms average map value = 0.3626, steps = 144 shifted from previous position = 14.3 rotated from previous position = 5.75 degrees atoms outside contour = 119148, contour level = 1.7351 Position of 7top.cif (#2) relative to cryosparc_P51_J28_003_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.94187225 0.29405715 0.16250249 -63.44801747 -0.08985543 0.68653751 -0.72152079 242.63156198 -0.32373240 0.66497868 0.67305326 27.00875393 Axis 0.91300212 0.32018295 -0.25280428 Axis point 0.00000000 96.39338650 288.66217751 Rotation angle (degrees) 49.40322263 Shift along axis 12.93038697 > hide #!2 models > volume #1 color #0096ff > volume #1 color #0096ff83 > volume #1 level 1.284 > open ""/Users/zhangj14 > (Deleted)/Downloads/cryosparc_P51_J30_004_volume_map_sharp.mrc"" Opened cryosparc_P51_J30_004_volume_map_sharp.mrc as #3, grid size 300,300,300, pixel 1.55, shown at level 0.921, step 2, values float32 > volume #3 step 1 > select #3 3 models selected > view matrix models #3,1,0,0,41.414,0,1,0,174.22,0,0,1,47.926 Drag select of 3 cryosparc_P51_J30_004_volume_map_sharp.mrc > view matrix models #3,1,0,0,42.712,0,1,0,65.405,0,0,1,-33.01 > volume #3 level 1.009 > select clear > volume #3 level 0.9648 > volume #3 level 0.9298 > volume #3 color #0433ff > volume #3 color #0433ff7c > volume #3 color #0433ff7d > set bgColor white > save ""/Users/zhangj14 (Deleted)/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v1.cxs"" > includeMaps true > show #!2 models > select /A25S:1734 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #2 125433 atoms, 135363 bonds, 3255 pseudobonds, 9795 residues, 4 models selected > select subtract #2 Nothing selected > select add #2 125433 atoms, 135363 bonds, 3255 pseudobonds, 9795 residues, 4 models selected > view matrix models > #2,0.94187,0.29406,0.1625,-48.381,-0.089855,0.68654,-0.72152,324.99,-0.32373,0.66498,0.67305,7.466 > view matrix models > #2,0.94187,0.29406,0.1625,-16.075,-0.089855,0.68654,-0.72152,206.16,-0.32373,0.66498,0.67305,126.84 > view matrix models > #2,0.94187,0.29406,0.1625,-16.044,-0.089855,0.68654,-0.72152,155,-0.32373,0.66498,0.67305,56.359 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.15743,-0.65047,-0.74304,578.88,-0.30321,-0.68424,0.66324,210.21,-0.93983,0.32971,-0.089511,399.63 > view matrix models > #2,0.7385,-0.67337,-0.034472,261.96,-0.19338,-0.26051,0.94591,46.014,-0.64593,-0.69188,-0.3226,593.66 > open 8CCS Summary of feedback from opening 8CCS fetched from pdb --- notes | Fetching compressed mmCIF 8ccs from http://files.rcsb.org/download/8ccs.cif Fetching CCD 1MA from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/A/1MA/1MA.cif Fetching CCD 4AC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/4AC/4AC.cif Fetching CCD 5MC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/5MC/5MC.cif Fetching CCD A2M from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/A2M/A2M.cif Fetching CCD B8N from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/B8N/B8N.cif Fetching CCD G7M from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/G7M/G7M.cif Fetching CCD MA6 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/6/MA6/MA6.cif Fetching CCD OMC from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/C/OMC/OMC.cif Fetching CCD OMG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/OMG/OMG.cif Fetching CCD OMU from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/U/OMU/OMU.cif Fetching CCD SPD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/SPD/SPD.cif Fetching CCD UR3 from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/3/UR3/UR3.cif Fetching CCD YYG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/YYG/YYG.cif 8ccs title: 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex [more info...] Chain information for 8ccs #4 --- Chain | Description | UniProt 0 | 40S ribosomal protein S24-A | RS24A_YEAST 1-135 1 | 40S ribosomal protein S25-A | RS25A_YEAST 1-108 2 | 40S ribosomal protein S26 | A0A6A5PUG0_YEASX 1-119 3 | 40S ribosomal protein S27-A | RS27A_YEAST 1-82 4 | 40S ribosomal protein S28-A | RS28A_YEAST 1-67 5 | HLJ1_G0030400.mRNA.1.CDS.1 | A0A6A5PV92_YEASX 1-56 6 | 40S ribosomal protein S30-A | RS30A_YEAST 1-63 7 | Guanine nucleotide-binding protein subunit beta-like protein | GBLP_YEAST 1-319 8 | Ubiquitin-40S ribosomal protein S31 | A0A6A5PU37_YEASX 1-152 A | 60S ribosomal protein L16-A | RL16A_YEAST 1-199 AA | 25S ribosomal RNA | B | 60S ribosomal protein L17-A | RL17A_YEAST 1-184 BB | 5S ribosomal RNA | Bb | Transfer RNA Phe | C | 60S ribosomal protein L18-A | RL18A_YEAST 1-186 CC | 5.8S ribosomal RNA | Cc | Transfer RNA fMet | D | 60S ribosomal protein L19-A | RL19A_YEAST 1-189 DD | 60S acidic ribosomal protein P0 | RLA0_YEAST 1-312 Dd | Messenger RNA | E | 60S ribosomal protein L20-A | RL20A_YEAST 1-172 EE | 60S ribosomal protein L2-A | RL2A_YEAST 1-254 Ee | 60S ribosomal protein L12-A | RL12A_YEAST 1-165 F | 60S ribosomal protein L21-A | RL21A_YEAST 1-160 FF | 60S ribosomal protein L3 | RL3_YEAST 1-387 G | 60S ribosomal protein L22-A | RL22A_YEAST 1-121 GG | 60S ribosomal protein L4-A | RL4A_YEAST 1-362 H | 60S ribosomal protein L23-A | RL23A_YEAST 1-137 HH | 60S ribosomal protein L5 | RL5_YEAST 1-297 I | 60S ribosomal protein L24-A | RL24A_YEAST 1-155 II | 60S ribosomal protein L6-A | RL6A_YEAST 1-176 J | 60S ribosomal protein L25 | RL25_YEAST 1-142 JJ | 60S ribosomal protein L7-A | RL7A_YEAST 1-244 K | 60S ribosomal protein L26-A | RL26A_YEAST 1-127 KK | 60S ribosomal protein L8-A | RL8A_YEAST 1-256 L | 60S ribosomal protein L27-A | RL27A_YEAST 1-136 LL | 60S ribosomal protein L9-A | RL9A_YEAST 1-191 M | 60S ribosomal protein L28 | RL28_YEAST 1-149 MM | 60S ribosomal protein L10 | RL10_YEAST 1-221 N | 60S ribosomal protein L29 | RL29_YEAST 1-59 NN | 60S ribosomal protein L11-A | RL11A_YEAST 1-174 O | 60S ribosomal protein L30 | RL30_YEAST 1-105 OO | 60S ribosomal protein L13-A | RL13A_YEAST 1-199 P | 60S ribosomal protein L31-A | RL31A_YEAST 1-113 PP | 60S ribosomal protein L14-A | RL14A_YEAST 1-138 Pp | di-peptide | Q | 60S ribosomal protein L32 | RL32_YEAST 1-130 QQ | 60S ribosomal protein L15-A | RL15A_YEAST 1-204 R | 60S ribosomal protein L33-A | RL33A_YEAST 1-107 S | 60S ribosomal protein L34-A | RL34A_YEAST 1-121 T | 60S ribosomal protein L35-A | RL35A_YEAST 1-120 U | 60S ribosomal protein L36-A | RL36A_YEAST 1-100 V | 60S ribosomal protein L37-A | RL37A_YEAST 1-88 W | 60S ribosomal protein L38 | RL38_YEAST 1-78 X | 60S ribosomal protein L39 | RL39_YEAST 1-51 Y | Ubiquitin-60S ribosomal protein L40 | RL40A_YEAST 1-128 Z | 60S ribosomal protein L41-A | RL41A_YEAST 1-25 a | 60S ribosomal protein L42-A | RL44A_YEAST 1-106 b | 60S ribosomal protein L43-A | RL43A_YEAST 1-92 c | 18S ribosomal RNA | d | 40S ribosomal protein S0-A | RSSA1_YEAST 1-252 e | 40S ribosomal protein S1-A | RS3A1_YEAS7 1-255 f | 40S ribosomal protein S2 | RS2_YEAST 1-254 g | RPS3 isoform 1 | A0A6A5Q3Q1_YEASX 1-240 h | 40S ribosomal protein S4-A | RS4A_YEAST 1-261 i | 40S ribosomal protein S5 | RS5_YEAST 1-225 j | 40S ribosomal protein S6-A | RS6A_YEAST 1-236 k | 40S ribosomal protein S7-A | RS7A_YEAST 1-190 l | 40S ribosomal protein S8-B | RS8B_YEAST 1-200 m | 40S ribosomal protein S9-A | RS9A_YEAST 1-197 n | 40S ribosomal protein S10-A | RS10A_YEAST 1-105 o | 40S ribosomal protein S11-A | RS11A_YEAST 1-156 p | 40S ribosomal protein S13 | RS13_YEAST 1-151 q | 40S ribosomal protein S14-A | RS14A_YEAST 1-137 r | 40S ribosomal protein S15 | RS15_YEAST 1-142 s | 40S ribosomal protein S16-A | RS16A_YEAST 1-143 t | 40S ribosomal protein S17-A | RS17A_YEAST 1-136 u | 40S ribosomal protein S18-A | RS18A_YEAST 1-146 v | 40S ribosomal protein S19-A | RS19A_YEAST 1-144 w | 40S ribosomal protein S20 | A0A6A5PVE9_YEASX 1-121 x | 40S ribosomal protein S21-A | RS21A_YEAST 1-87 y | 40S ribosomal protein S22-A | RS22A_YEAST 1-130 z | 40S ribosomal protein S23-A | RS23A_YEAST 1-145 Non-standard residues in 8ccs #4 --- B8N — (2~{R})-2-azanyl-4-[5-[(2~{S},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-3-methyl-2,6-bis(oxidanylidene)pyrimidin-1-yl]butanoic acid K — potassium ion MG — magnesium ion SPD — spermidine (N-(2-amino-propyl)-1,4-diaminobutane; Pa(34)) ZN — zinc ion > hide sel atoms > show sel cartoons > hide #!2 models > select subtract #2 Nothing selected > hide #!4 models > show #!4 models > nucleotides #!4 atoms > style nucleic & #!4 stick Changed 112013 atom styles > hide #!4 atoms > show #!4 cartoons > select #4/AA:978 23 atoms, 25 bonds, 1 residue, 1 model selected > select add #4 201697 atoms, 215006 bonds, 6540 pseudobonds, 17908 residues, 4 models selected > view matrix models > #4,-0.30464,0.5358,-0.78747,419.87,-0.92389,0.03476,0.38107,410.09,0.23155,0.84363,0.48443,-153.24 > view matrix models > #4,0.85587,0.51644,-0.027796,-94.582,-0.47758,0.8098,0.3408,88.636,0.19851,-0.2784,0.93973,38.738 > view matrix models > #4,0.08915,0.71993,-0.68829,236.22,-0.96445,0.23499,0.12088,436.92,0.24877,0.65305,0.71529,-168.44 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.08915,0.71993,-0.68829,295.31,-0.96445,0.23499,0.12088,304.27,0.24877,0.65305,0.71529,-25.517 > view matrix models > #4,0.08915,0.71993,-0.68829,306.56,-0.96445,0.23499,0.12088,289.54,0.24877,0.65305,0.71529,-5.9918 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.65825,-0.75262,0.016467,363.86,0.7524,0.65846,0.018203,-262.41,-0.024543,0.00040782,0.9997,169.05 > view matrix models > #4,0.0082103,-0.91944,-0.39315,696.24,0.8551,0.21028,-0.4739,-34.279,0.51839,-0.3323,0.78794,170.6 > view matrix models > #4,0.49911,-0.84609,-0.18716,487.63,0.85242,0.51822,-0.069464,-227.36,0.15576,-0.12487,0.97987,159.91 > view matrix models > #4,0.78277,-0.62183,0.024392,292.32,0.62229,0.78242,-0.023882,-249.69,-0.0042348,0.033873,0.99942,154.49 > view matrix models > #4,0.84679,0.43289,-0.30911,77.328,-0.45595,0.29142,-0.84094,397.51,-0.27395,0.85304,0.44415,154.21 > view matrix models > #4,0.5428,0.70459,-0.45707,125.41,-0.83478,0.39284,-0.38578,348.77,-0.092263,0.59095,0.80141,79.805 > view matrix models > #4,0.39742,0.78381,-0.47718,148.52,-0.90105,0.23491,-0.36459,404.08,-0.17368,0.57486,0.79961,106.7 > view matrix models > #4,0.53496,0.76611,-0.35623,83.375,-0.84447,0.4717,-0.25371,294.03,-0.026333,0.43655,0.89929,77.616 > ui mousemode right ""translate selected models"" > view matrix models > #4,0.53496,0.76611,-0.35623,-0.25029,-0.84447,0.4717,-0.25371,455.1,-0.026333,0.43655,0.89929,-164.88 > view matrix models > #4,0.53496,0.76611,-0.35623,7.6398,-0.84447,0.4717,-0.25371,460.32,-0.026333,0.43655,0.89929,-161.22 > view matrix models > #4,0.53496,0.76611,-0.35623,7.065,-0.84447,0.4717,-0.25371,472.76,-0.026333,0.43655,0.89929,-163.65 > view matrix models > #4,0.53496,0.76611,-0.35623,6.1842,-0.84447,0.4717,-0.25371,471.71,-0.026333,0.43655,0.89929,-160.45 > fitmap #4 inMap #3 Fit molecule 8ccs (#4) to map cryosparc_P51_J30_004_volume_map_sharp.mrc (#3) using 201697 atoms average map value = 0.3242, steps = 140 shifted from previous position = 13.2 rotated from previous position = 9.4 degrees atoms outside contour = 174799, contour level = 0.92983 Position of 8ccs (#4) relative to cryosparc_P51_J30_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.61327937 0.75684858 -0.22598371 -80.64572258 -0.77773143 0.52865799 -0.34008022 390.79789583 -0.13792114 0.38431882 0.91283997 -79.64002910 Axis 0.42630559 -0.05182443 -0.90309345 Axis point 330.73846119 285.28803133 0.00000000 Rotation angle (degrees) 58.17081343 Shift along axis 17.28978881 > view matrix models > #4,0.61328,0.75685,-0.22598,86.167,-0.77773,0.52866,-0.34008,276.32,-0.13792,0.38432,0.91284,-143.95 > view matrix models > #4,0.61328,0.75685,-0.22598,86.863,-0.77773,0.52866,-0.34008,241.08,-0.13792,0.38432,0.91284,-119.51 > ui mousemode right ""rotate selected models"" > view matrix models > #4,0.78661,-0.60007,-0.14547,388.86,0.61703,0.77261,0.1495,-335.37,0.022682,-0.20736,0.978,-18.966 > view matrix models > #4,-0.93576,-0.16159,0.31343,610.22,-0.072479,0.95799,0.2775,-234.34,-0.3451,0.23696,-0.90816,470.6 > view matrix models > #4,-0.39924,-0.87006,0.28914,665.31,-0.91613,0.36607,-0.16341,275,0.036338,-0.33013,-0.94324,531.92 > view matrix models > #4,-0.046058,-0.99795,0.044359,671.16,-0.77851,0.0080341,-0.62758,461.49,0.62594,-0.063439,-0.77729,254.68 > view matrix models > #4,-0.67415,-0.68926,-0.2654,840.63,-0.59799,0.72027,-0.35159,143.27,0.4335,-0.078318,-0.89775,343.43 > ui mousemode right ""translate selected models"" > view matrix models > #4,-0.67415,-0.68926,-0.2654,701.6,-0.59799,0.72027,-0.35159,352.46,0.4335,-0.078318,-0.89775,332.61 > view matrix models > #4,-0.67415,-0.68926,-0.2654,704.41,-0.59799,0.72027,-0.35159,341.63,0.4335,-0.078318,-0.89775,344.13 > view matrix models > #4,-0.67415,-0.68926,-0.2654,720.57,-0.59799,0.72027,-0.35159,346.87,0.4335,-0.078318,-0.89775,338.99 > view matrix models > #4,-0.67415,-0.68926,-0.2654,716.3,-0.59799,0.72027,-0.35159,354.68,0.4335,-0.078318,-0.89775,341.07 > fitmap #4 inMap #3 Fit molecule 8ccs (#4) to map cryosparc_P51_J30_004_volume_map_sharp.mrc (#3) using 201697 atoms average map value = 0.7965, steps = 340 shifted from previous position = 9.96 rotated from previous position = 36.3 degrees atoms outside contour = 125413, contour level = 0.92983 Position of 8ccs (#4) relative to cryosparc_P51_J30_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation -0.94386421 -0.31230302 0.10764374 539.62589137 -0.32537200 0.93520865 -0.13970629 106.53858828 -0.05703866 -0.16688803 -0.98432463 560.71405021 Axis -0.16235518 0.98363986 -0.07806040 Axis point 290.51169275 0.00000000 273.17526891 Rotation angle (degrees) 175.19810990 Shift along axis -26.58501715 > select clear > volume #3 level 0.7986 > hide #!4 models > show #!4 models > save ""/Users/zhangj14 (Deleted)/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v1.cxs"" > includeMaps true > save ""/Users/zhangj14 (Deleted)/Desktop/image1.png"" supersample 3 > movie record > turn y 2 180 > wait 180 > movie encode ""/Users/zhangj14 (Deleted)/Desktop/movie1.mp4"" Movie saved to /Users/zhangj14 (Deleted)/Desktop/movie1.mp4 > volume #3 level 0.8861 > show #!4 atoms > style #!4 stick Changed 201697 atom styles > volume #3 level 0.6626 > volume #3 level 0.769 > save ""/Users/zhangj14 (Deleted)/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v1.cxs"" > includeMaps true ——— End of log from Thu Aug 7 18:58:25 2025 ——— opened ChimeraX session > open ""/Users/zhangj14 (Deleted)/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/cryosparc_P51_J40_map_sharp.mrc"" Opened cryosparc_P51_J40_map_sharp.mrc as #5, grid size 700,700,700, pixel 0.93, shown at step 1, values float32 > volume #5 level -9.265e-06,0 level 0.1272,0.8 level 1.726,1 > volume #5 region 0,0,0,699,699,699 step 4 [Repeated 1 time(s)] > volume #5 level 0.0722 > volume #5 color #ff40ff > volume #5 color #ff40ff82 > volume #5 step 2 Drag select of 5 cryosparc_P51_J40_map_sharp.mrc > ui mousemode right ""translate selected models"" > view matrix models #5,1,0,0,-91.967,0,1,0,196.26,0,0,1,-182.27 > view matrix models #5,1,0,0,-73.35,0,1,0,199.08,0,0,1,-198.02 > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models #5,1,0,0,-46.563,0,1,0,-33.52,0,0,1,-114.05 > select add #5 5 models selected > select add #5 5 models selected > select add #5 5 models selected > select add #5 5 models selected > hide #!4 models > fitmap #5 inMap #3 Fit map cryosparc_P51_J40_map_sharp.mrc in map cryosparc_P51_J30_004_volume_map_sharp.mrc using 169901 points correlation = 0.8787, correlation about mean = 0.6972, overlap = 7.071e+04 steps = 156, shift = 7.13, angle = 16.4 degrees Position of cryosparc_P51_J40_map_sharp.mrc (#5) relative to cryosparc_P51_J30_004_volume_map_sharp.mrc (#3) coordinates: Matrix rotation and translation 0.96857314 -0.24261307 -0.05481755 10.60702797 0.24785332 0.95990789 0.13094114 -202.04971599 0.02085177 -0.14041278 0.98987345 -43.31356925 Axis -0.47975340 -0.13378326 0.86714400 Axis point 808.75885917 -91.92424921 0.00000000 Rotation angle (degrees) 16.42772453 Shift along axis -15.61698922 > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!3 models > volume #5 color #0096ff > volume #5 color #76d6ff > volume #5 color #7a81ff > volume #5 step 1 > volume #5 level 0.119 > select clear > show #!4 models > volume #5 color #7a81ff7d Drag select of 250 atoms, 63 residues, 12 pseudobonds, 232 bonds, 5 cryosparc_P51_J40_map_sharp.mrc > select clear > ui tool show ""Side View"" > hide #!4 atoms Drag select of 111 residues, 5 cryosparc_P51_J40_map_sharp.mrc > select clear > volume #5 level 0.09347 > save ""/Users/zhangj14 (Deleted)/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"" > includeMaps true ——— End of log from Fri Aug 8 16:22:56 2025 ——— opened ChimeraX session > view > ui tool show ""Side View"" > volume #5 level 0.3563 > close #3 > close #1 > volume #5 level 0.1946 > color #4 #942193ff > hide #!4 cartoons > show #!4 atoms > hide #!4 models > show #!2 models > hide #!2 models > show #!4 models > style #!4 ball Changed 201697 atom styles > color #!4 byhetero > rainbow #!4 > color #!4 byhetero > nucleotides #!4 atoms > style nucleic & #!4 stick Changed 112013 atom styles > show #!4 cartoons > hide #!4 atoms > nucleotides #!4 atoms > style nucleic & #!4 stick Changed 112013 atom styles > nucleotides #!4 atoms > style nucleic & #!4 stick Changed 112013 atom styles > nucleotides #!4 atoms > style nucleic & #!4 stick Changed 112013 atom styles > nucleotides #!4 fill > style nucleic & #!4 stick Changed 112013 atom styles > nucleotides #!4 fill > style nucleic & #!4 stick Changed 112013 atom styles > nucleotides #!4 ladder > nucleotides #!4 stubs > select add #4 201697 atoms, 215006 bonds, 6540 pseudobonds, 17908 residues, 4 models selected > nucleotides sel stubs > nucleotides sel atoms > style nucleic & sel stick Changed 112013 atom styles > show sel atoms > style sel stick Changed 201697 atom styles > hide sel atoms > save ""/Users/zhangj14/Google Drive/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"" > volume #5 level 0.1564 > volume #5 level 0.09679 > volume #5 color darkgrey > volume #5 color #a9a9a976 > volume #5 color #a9a9a975 > volume #5 color #797979 > volume #5 color #79797976 > volume #5 color #ebebeb > volume #5 color #ebebeb83 > show sel atoms > hide sel atoms > lighting simple > lighting full > save ""/Users/zhangj14/Google Drive/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/080725_yeast_ribosomes_WT_P51_v2.cxs"" ——— End of log from Sun Aug 10 00:06:22 2025 ——— opened ChimeraX session > open ""/Users/zhangj14/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/cryosparc_P51_J67_003_volume_map_sharp.mrc"" Opened cryosparc_P51_J67_003_volume_map_sharp.mrc as #1, grid size 512,512,512, pixel 0.93, shown at level 0.357, step 2, values float32 > volume #1 level 0.5205 > select subtract #4 Nothing selected > hide #!4 models > hide #!1 models > show #!1 models > color #1 #008f00ff models > color #1 #008f0087 models > select #1 2 models selected > ui mousemode right ""translate selected models"" > view matrix models #1,1,0,0,44.72,0,1,0,-2.3368,0,0,1,-230.93 > view matrix models #1,1,0,0,51.117,0,1,0,-21.257,0,0,1,-218.17 > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.12973,0.99149,0.011016,1.0388,-0.85062,0.10557,0.51506,302.26,0.50952,-0.076189,0.85708,-289.64 > view matrix models > #1,0.014963,-0.07744,-0.99688,524.05,-0.20749,-0.97554,0.072667,523.74,-0.97812,0.20575,-0.030664,187.2 > view matrix models > #1,0.33833,0.91583,-0.21629,19.95,-0.065775,-0.20626,-0.97628,518.66,-0.93873,0.34453,-0.0095464,137.26 > view matrix models > #1,-0.60235,0.6319,-0.48773,378.04,0.023864,-0.59649,-0.80227,560.29,-0.79788,-0.49488,0.34421,243.74 > view matrix models > #1,-0.71226,0.57949,-0.39609,398.06,-0.22009,-0.72021,-0.65792,619.45,-0.66652,-0.38144,0.64051,118.5 > view matrix models > #1,-0.51225,0.23374,-0.82642,533.01,-0.039985,-0.9677,-0.24891,551.39,-0.85791,-0.094459,0.50505,119.62 > view matrix models > #1,-0.37195,0.13187,0.91884,146.5,-0.91248,0.12978,-0.388,507.05,-0.17041,-0.98274,0.072056,278.53 > hide #!1 models > select subtract #1 Nothing selected > show #!4 models > volume #1 level 0.4781 > volume #5 level 0.08828 > volume #5 level 0.07552 > split #4 Split 8ccs (#4) into 83 models Chain information for 8ccs 0 #4.1 --- Chain | Description 0 | No description available Chain information for 8ccs 1 #4.2 --- Chain | Description 1 | No description available Chain information for 8ccs 2 #4.3 --- Chain | Description 2 | No description available Chain information for 8ccs 3 #4.4 --- Chain | Description 3 | No description available Chain information for 8ccs 4 #4.5 --- Chain | Description 4 | No description available Chain information for 8ccs 5 #4.6 --- Chain | Description 5 | No description available Chain information for 8ccs 6 #4.7 --- Chain | Description 6 | No description available Chain information for 8ccs 7 #4.8 --- Chain | Description 7 | No description available Chain information for 8ccs 8 #4.9 --- Chain | Description 8 | No description available Chain information for 8ccs A #4.10 --- Chain | Description A | No description available Chain information for 8ccs AA #4.11 --- Chain | Description AA | No description available Chain information for 8ccs B #4.12 --- Chain | Description B | No description available Chain information for 8ccs BB #4.13 --- Chain | Description BB | No description available Chain information for 8ccs Bb #4.14 --- Chain | Description Bb | No description available Chain information for 8ccs C #4.15 --- Chain | Description C | No description available Chain information for 8ccs CC #4.16 --- Chain | Description CC | No description available Chain information for 8ccs Cc #4.17 --- Chain | Description Cc | No description available Chain information for 8ccs D #4.18 --- Chain | Description D | No description available Chain information for 8ccs DD #4.19 --- Chain | Description DD | No description available Chain information for 8ccs Dd #4.20 --- Chain | Description Dd | No description available Chain information for 8ccs E #4.21 --- Chain | Description E | No description available Chain information for 8ccs EE #4.22 --- Chain | Description EE | No description available Chain information for 8ccs Ee #4.23 --- Chain | Description Ee | No description available Chain information for 8ccs F #4.24 --- Chain | Description F | No description available Chain information for 8ccs FF #4.25 --- Chain | Description FF | No description available Chain information for 8ccs G #4.26 --- Chain | Description G | No description available Chain information for 8ccs GG #4.27 --- Chain | Description GG | No description available Chain information for 8ccs H #4.28 --- Chain | Description H | No description available Chain information for 8ccs HH #4.29 --- Chain | Description HH | No description available Chain information for 8ccs I #4.30 --- Chain | Description I | No description available Chain information for 8ccs II #4.31 --- Chain | Description II | No description available Chain information for 8ccs J #4.32 --- Chain | Description J | No description available Chain information for 8ccs JJ #4.33 --- Chain | Description JJ | No description available Chain information for 8ccs K #4.34 --- Chain | Description K | No description available Chain information for 8ccs KK #4.35 --- Chain | Description KK | No description available Chain information for 8ccs L #4.36 --- Chain | Description L | No description available Chain information for 8ccs LL #4.37 --- Chain | Description LL | No description available Chain information for 8ccs M #4.38 --- Chain | Description M | No description available Chain information for 8ccs MM #4.39 --- Chain | Description MM | No description available Chain information for 8ccs N #4.40 --- Chain | Description N | No description available Chain information for 8ccs NN #4.41 --- Chain | Description NN | No description available Chain information for 8ccs O #4.42 --- Chain | Description O | No description available Chain information for 8ccs OO #4.43 --- Chain | Description OO | No description available Chain information for 8ccs P #4.44 --- Chain | Description P | No description available Chain information for 8ccs PP #4.45 --- Chain | Description PP | No description available Chain information for 8ccs Pp #4.46 --- Chain | Description Pp | No description available Chain information for 8ccs Q #4.47 --- Chain | Description Q | No description available Chain information for 8ccs QQ #4.48 --- Chain | Description QQ | No description available Chain information for 8ccs R #4.49 --- Chain | Description R | No description available Chain information for 8ccs S #4.50 --- Chain | Description S | No description available Chain information for 8ccs T #4.51 --- Chain | Description T | No description available Chain information for 8ccs U #4.52 --- Chain | Description U | No description available Chain information for 8ccs V #4.53 --- Chain | Description V | No description available Chain information for 8ccs W #4.54 --- Chain | Description W | No description available Chain information for 8ccs X #4.55 --- Chain | Description X | No description available Chain information for 8ccs Y #4.56 --- Chain | Description Y | No description available Chain information for 8ccs Z #4.57 --- Chain | Description Z | No description available Chain information for 8ccs a #4.58 --- Chain | Description a | No description available Chain information for 8ccs b #4.59 --- Chain | Description b | No description available Chain information for 8ccs c #4.60 --- Chain | Description c | No description available Chain information for 8ccs d #4.61 --- Chain | Description d | No description available Chain information for 8ccs e #4.62 --- Chain | Description e | No description available Chain information for 8ccs f #4.63 --- Chain | Description f | No description available Chain information for 8ccs g #4.64 --- Chain | Description g | No description available Chain information for 8ccs h #4.65 --- Chain | Description h | No description available Chain information for 8ccs i #4.66 --- Chain | Description i | No description available Chain information for 8ccs j #4.67 --- Chain | Description j | No description available Chain information for 8ccs k #4.68 --- Chain | Description k | No description available Chain information for 8ccs l #4.69 --- Chain | Description l | No description available Chain information for 8ccs m #4.70 --- Chain | Description m | No description available Chain information for 8ccs n #4.71 --- Chain | Description n | No description available Chain information for 8ccs o #4.72 --- Chain | Description o | No description available Chain information for 8ccs p #4.73 --- Chain | Description p | No description available Chain information for 8ccs q #4.74 --- Chain | Description q | No description available Chain information for 8ccs r #4.75 --- Chain | Description r | No description available Chain information for 8ccs s #4.76 --- Chain | Description s | No description available Chain information for 8ccs t #4.77 --- Chain | Description t | No description available Chain information for 8ccs u #4.78 --- Chain | Description u | No description available Chain information for 8ccs v #4.79 --- Chain | Description v | No description available Chain information for 8ccs w #4.80 --- Chain | Description w | No description available Chain information for 8ccs x #4.81 --- Chain | Description x | No description available Chain information for 8ccs y #4.82 --- Chain | Description y | No description available Chain information for 8ccs z #4.83 --- Chain | Description z | No description available > select add #4.83 1122 atoms, 1139 bonds, 145 residues, 1 model selected > select subtract #4.83 Nothing selected > select add #4.83 1122 atoms, 1139 bonds, 145 residues, 1 model selected > volume #5 level 0.1138 > volume #5 color #ebebebb6 > volume #5 color #ebebebda > volume #5 color #011993 > volume #5 color #011993cc > volume #5 color #011993b1 > volume #5 color #011993b0 > volume #5 level 0.08403 > view sel > ui tool show ""Side View"" > lighting shadows false > hide #4.83 models > show #4.83 models > hide #4.83 models > show #4.83 models > hide #!4 models > select subtract #4.83 Nothing selected > select add #4.83 1122 atoms, 1139 bonds, 145 residues, 1 model selected > show #!4 models > hide #4.1 models > hide #4.2 models > hide #!4.3 models > hide #4.4 models > hide #4.5 models > hide #!4.6 models > hide #4.7 models > hide #4.8 models > hide #!4.9 models > hide #4.10 models > hide #!4.11 models > hide #!4.12 models > show #!4.11 models > hide #!4.11 models > hide #!4.13 models > hide #!4.14 models > show #!4.14 models > hide #4.15 models > hide #!4.16 models > hide #!4.17 models > hide #4.18 models > show #!4.17 models > hide #4.19 models > hide #!4.20 models > hide #4.21 models > hide #!4.22 models > hide #4.23 models > hide #4.24 models > hide #!4.25 models > hide #4.26 models > hide #4.27 models > hide #!4.28 models > hide #4.29 models > hide #4.30 models > hide #!4.31 models > hide #4.32 models > hide #4.33 models > hide #4.34 models > hide #4.35 models > hide #4.36 models > hide #4.37 models > hide #4.38 models > hide #!4.39 models > hide #4.40 models > show #4.38 models > hide #4.38 models > hide #4.41 models > show #4.41 models > hide #4.41 models > hide #4.42 models > hide #4.43 models > hide #4.44 models > hide #4.45 models > hide #4.46 models > hide #!4.47 models > hide #!4.48 models > hide #4.49 models > hide #!4.50 models > hide #4.51 models > hide #4.52 models > hide #!4.53 models > hide #4.54 models > hide #4.55 models > hide #!4.56 models > hide #4.57 models > hide #!4.58 models > hide #!4.59 models > hide #!4.60 models > show #!4.60 models > hide #4.61 models > hide #4.62 models > hide #4.63 models > hide #4.64 models > hide #4.65 models > hide #!4.66 models > hide #4.67 models > show #4.67 models > hide #4.67 models > hide #4.68 models > hide #!4.69 models > hide #4.70 models > show #4.70 models > hide #4.70 models > hide #4.71 models > hide #4.72 models > hide #4.73 models > hide #!4.74 models > hide #!4.75 models > hide #4.76 models > hide #4.77 models > hide #4.78 models > show #4.78 models > hide #4.78 models > hide #4.79 models > hide #4.80 models > hide #4.81 models > hide #4.82 models > hide #4.83 models > show #4.83 models > hide #!5 models > show #!5 models > save ""/Users/zhangj14/Google Drive/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/081125_yeast_ribosomes_WT_P51_v3_zoom_S12.cxs"" > includeMaps true > color #4 #919191ff models > color #4 #fffb00ff models > color #4 #945200ff models > color #4.83 #942193ff > select subtract #4.83 Nothing selected > volume #5 level 0.05425 > show #!4.20 models > color #4.20 #00f900ff > color #4.20 #00fdffff > select add #4.17 1651 atoms, 1836 bonds, 82 pseudobonds, 84 residues, 3 models selected > select subtract #4.17 Nothing selected > select add #4.14 1644 atoms, 1831 bonds, 74 pseudobonds, 82 residues, 3 models selected > color #4.14 #00f900ff > select subtract #4.14 Nothing selected > save ""/Users/zhangj14/Google Drive/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/081125_yeast_ribosomes_WT_P51_v3_zoom_S12.cxs"" > includeMaps true > volume #5 level 0.04574 > select add #4.20 283 atoms, 311 bonds, 2 pseudobonds, 18 residues, 2 models selected > select subtract #4.20 Nothing selected > select add #4.20 283 atoms, 311 bonds, 2 pseudobonds, 18 residues, 2 models selected > show sel atoms > select subtract #4.20 Nothing selected > hide #!4.60 models > show #!4.60 models > color #4.60 #7a81ffff > color #4.60 #5254ffff > color #4.60 #81c4ffff > color #4.60 #ff3a2cff > color #4.60 #ff4486ff > color #4.60 #fff61eff > color #4.60 #4bff26ff > color #4.60 #b31cffff > color #4.60 #d627ffff > color #4.60 #55fff5ff > color #4.60 #26ff3dff > color #4.60 #ff9517ff > save ""/Users/zhangj14/Google Drive/My Drive/Cryo- > EM/2025_Ribosomes/080725_WT_Glacios/081125_yeast_ribosomes_WT_P51_v3_zoom_S12.cxs"" ——— End of log from Mon Aug 11 01:17:32 2025 ——— > view name session-start opened ChimeraX session > volume #5 level 0.02447 > sequence chain #2/A25S Alignment identifier is 2/A25S > sequence chain #2/A58S#4.16/CC Alignment identifier is 1 > sequence chain #2/A5S#4.13/BB Alignment identifier is 2 > sequence chain #2/AL02 Alignment identifier is 2/AL02 > sequence chain #2/AL03 Alignment identifier is 2/AL03 > sequence chain #2/AL04 Alignment identifier is 2/AL04 > sequence chain #2/AL05 Alignment identifier is 2/AL05 > sequence chain #2/AL06 Alignment identifier is 2/AL06 > sequence chain #2/AL07 Alignment identifier is 2/AL07 > sequence chain #2/AL08 Alignment identifier is 2/AL08 > sequence chain #2/AL09#4.37/LL Alignment identifier is 3 > sequence chain #2/AL10 Alignment identifier is 2/AL10 > sequence chain #2/AL11 Alignment identifier is 2/AL11 > sequence chain #2/AL12 Alignment identifier is 2/AL12 > sequence chain #2/AL13 Alignment identifier is 2/AL13 > sequence chain #2/AL14 Alignment identifier is 2/AL14 > sequence chain #2/AL15 Alignment identifier is 2/AL15 > sequence chain #2/AL16 Alignment identifier is 2/AL16 > sequence chain #2/AL17 Alignment identifier is 2/AL17 > sequence chain #2/AL18 Alignment identifier is 2/AL18 > sequence chain #2/AL19 Alignment identifier is 2/AL19 > sequence chain #2/AL20#4.21/E Alignment identifier is 4 > sequence chain #2/AL21 Alignment identifier is 2/AL21 > sequence chain #2/AL22 Alignment identifier is 2/AL22 > sequence chain #2/AL23 Alignment identifier is 2/AL23 > sequence chain #2/AL24 Alignment identifier is 2/AL24 > sequence chain #2/AL25 Alignment identifier is 2/AL25 > sequence chain #2/AL26 Alignment identifier is 2/AL26 > sequence chain #2/AL27 Alignment identifier is 2/AL27 > sequence chain #2/AL28 Alignment identifier is 2/AL28 > sequence chain #2/AL29 Alignment identifier is 2/AL29 > sequence chain #2/AL30 Alignment identifier is 2/AL30 > sequence chain #2/AL31 Alignment identifier is 2/AL31 > sequence chain #2/AL32 Alignment identifier is 2/AL32 > sequence chain #2/AL33 Alignment identifier is 2/AL33 > sequence chain #2/AL34 Alignment identifier is 2/AL34 > sequence chain #2/AL35 Alignment identifier is 2/AL35 > sequence chain #2/AL36 Alignment identifier is 2/AL36 > sequence chain #2/AL37 Alignment identifier is 2/AL37 > sequence chain #2/AL38 Alignment identifier is 2/AL38 > sequence chain #2/AL39 Alignment identifier is 2/AL39 > sequence chain #2/AL40 Alignment identifier is 2/AL40 > sequence chain #2/AL41#4.57/Z Alignment identifier is 5 > sequence chain #2/AL42 Alignment identifier is 2/AL42 > sequence chain #2/AL43 Alignment identifier is 2/AL43 > sequence chain #2/ALP0 Alignment identifier is 2/ALP0 > sequence chain #2/APTN Alignment identifier is 2/APTN > sequence chain #2/PR Alignment identifier is 2/PR > sequence chain #4.1/0 Alignment identifier is 4.1/0 > sequence chain #4.2/1 Alignment identifier is 4.2/1 > sequence chain #4.3/2 Alignment identifier is 4.3/2 > sequence chain #4.4/3 Alignment identifier is 4.4/3 > sequence chain #4.5/4 Alignment identifier is 4.5/4 > sequence chain #4.6/5 Alignment identifier is 4.6/5 > sequence chain #4.7/6 Alignment identifier is 4.7/6 > sequence chain #4.8/7 Alignment identifier is 4.8/7 > sequence chain #4.9/8 Alignment identifier is 4.9/8 > sequence chain #4.10/A Alignment identifier is 4.10/A > sequence chain #4.11/AA Alignment identifier is 4.11/AA > sequence chain #4.12/B Alignment identifier is 4.12/B > sequence chain #4.14/Bb Alignment identifier is 4.14/Bb > sequence chain #4.15/C Alignment identifier is 4.15/C > sequence chain #4.17/Cc Alignment identifier is 4.17/Cc > sequence chain #4.18/D Alignment identifier is 4.18/D > sequence chain #4.19/DD Alignment identifier is 4.19/DD > sequence chain #4.20/Dd Alignment identifier is 4.20/Dd > sequence chain #4.22/EE Alignment identifier is 4.22/EE > sequence chain #4.23/Ee Alignment identifier is 4.23/Ee > sequence chain #4.24/F Alignment identifier is 4.24/F > sequence chain #4.25/FF Alignment identifier is 4.25/FF > sequence chain #4.26/G Alignment identifier is 4.26/G > sequence chain #4.27/GG Alignment identifier is 4.27/GG > sequence chain #4.28/H Alignment identifier is 4.28/H > sequence chain #4.29/HH Alignment identifier is 4.29/HH > sequence chain #4.30/I Alignment identifier is 4.30/I > sequence chain #4.31/II Alignment identifier is 4.31/II > sequence chain #4.32/J Alignment identifier is 4.32/J > sequence chain #4.33/JJ Alignment identifier is 4.33/JJ > sequence chain #4.34/K Alignment identifier is 4.34/K > sequence chain #4.35/KK Alignment identifier is 4.35/KK > sequence chain #4.36/L Alignment identifier is 4.36/L > sequence chain #4.38/M Alignment identifier is 4.38/M > sequence chain #4.39/MM Alignment identifier is 4.39/MM > sequence chain #4.40/N Alignment identifier is 4.40/N > sequence chain #4.41/NN Alignment identifier is 4.41/NN > sequence chain #4.42/O Alignment identifier is 4.42/O > sequence chain #4.43/OO Alignment identifier is 4.43/OO > sequence chain #4.44/P Alignment identifier is 4.44/P > sequence chain #4.45/PP Alignment identifier is 4.45/PP > sequence chain #4.46/Pp Alignment identifier is 4.46/Pp > sequence chain #4.47/Q Alignment identifier is 4.47/Q > sequence chain #4.48/QQ Alignment identifier is 4.48/QQ > sequence chain #4.49/R Alignment identifier is 4.49/R > sequence chain #4.50/S Alignment identifier is 4.50/S > sequence chain #4.51/T Alignment identifier is 4.51/T > sequence chain #4.52/U Alignment identifier is 4.52/U > sequence chain #4.53/V Alignment identifier is 4.53/V > sequence chain #4.54/W Alignment identifier is 4.54/W > sequence chain #4.55/X Alignment identifier is 4.55/X > sequence chain #4.56/Y Alignment identifier is 4.56/Y > sequence chain #4.58/a Alignment identifier is 4.58/a > sequence chain #4.59/b Alignment identifier is 4.59/b > sequence chain #4.60/c Alignment identifier is 4.60/c > sequence chain #4.61/d Alignment identifier is 4.61/d > sequence chain #4.62/e Alignment identifier is 4.62/e > sequence chain #4.63/f Alignment identifier is 4.63/f > sequence chain #4.64/g Alignment identifier is 4.64/g > sequence chain #4.65/h Alignment identifier is 4.65/h > sequence chain #4.66/i Alignment identifier is 4.66/i > sequence chain #4.67/j Alignment identifier is 4.67/j > sequence chain #4.68/k Alignment identifier is 4.68/k > sequence chain #4.69/l Alignment identifier is 4.69/l > sequence chain #4.70/m Alignment identifier is 4.70/m > sequence chain #4.71/n Alignment identifier is 4.71/n > sequence chain #4.72/o Alignment identifier is 4.72/o > sequence chain #4.73/p Alignment identifier is 4.73/p > sequence chain #4.74/q Alignment identifier is 4.74/q > sequence chain #4.75/r Alignment identifier is 4.75/r > sequence chain #4.76/s Alignment identifier is 4.76/s > sequence chain #4.77/t Alignment identifier is 4.77/t > sequence chain #4.78/u Alignment identifier is 4.78/u > sequence chain #4.79/v Alignment identifier is 4.79/v > sequence chain #4.80/w Alignment identifier is 4.80/w > sequence chain #4.81/x Alignment identifier is 4.81/x > sequence chain #4.82/y Alignment identifier is 4.82/y > sequence chain #4.83/z Alignment identifier is 4.83/z ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11 (2025-12-17) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/zhangj14/My Drive/Cryo- > EM/2025_Ribosomes/092625_K62_Krios/cryosparc_P52_J153_map_sharp.mrc"" Opened cryosparc_P52_J153_map_sharp.mrc as #1, grid size 512,512,512, pixel 0.93, shown at level 0.0831, step 2, values float32 OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: Mac Studio Model Identifier: Mac13,1 Model Number: Z14J000H2LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 13822.61.10 OS Loader Version: 11881.140.96 Software: System Software Overview: System Version: macOS 15.7.3 (24G419) Kernel Version: Darwin 24.6.0 Time since boot: 1 day, 3 hours, 40 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Studio Display: Display Type: Retina LCD Resolution: 5120 x 2880 Retina Display Serial Number: JD71PFVWLJ Display Firmware Version: Version 17.0 (Build 21A329) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 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: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.11 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.25.1 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.2.5 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pytz: 2025.2 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.0.0 roman-numerals-py: 4.0.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.0.4 stack-data: 0.6.3 starlette: 0.50.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 tzdata: 2025.3 urllib3: 2.6.2 uvicorn: 0.38.0 wcwidth: 0.2.14 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX