id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15200 Crash changing Mac display configuration chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.4.1-arm64-arm-64bit ChimeraX Version: 1.8.dev202403220040 (2024-03-22 00:40:30 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Thread 0x000000031887f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000317873000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000316867000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031585b000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031484f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000313843000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000312837000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031182b000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031081f000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030f813000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000030e807000 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001fa9f3ac0 (most recent call first): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 280 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.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, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath (total: 53) {""app_name"":""ChimeraX"",""timestamp"":""2024-05-14 11:48:41.00 +0200"",""app_version"":""1.8.0"",""slice_uuid"":""17982d98-65bc-3327-8526-577ec996453c"",""build_version"":""1.8.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.4.1 (23E224)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""CF26F3C4-D6DC-404C-956D-8E8C5CA2CB47""} { ""uptime"" : 52000, ""procRole"" : ""Background"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,3"", ""coalitionID"" : 4270, ""osVersion"" : { ""train"" : ""macOS 14.4.1"", ""build"" : 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""rollouts"" : [ { ""rolloutId"" : ""63f9578e238e7b23a1f3030a"", ""factorPackIds"" : { }, ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""64c025b28b7f0e739e4fbe58"", ""factorPackIds"" : { }, ""deploymentId"" : 240000019 } ], ""experiments"" : [ { ""treatmentId"" : ""a34d22a1-a1a5-4126-a477-0c499e502c6a"", ""experimentId"" : ""65835bc103dc58766bab2d27"", ""deploymentId"" : 400000011 }, { ""treatmentId"" : ""5d85d104-adc7-4ebf-8b7c-96d84fdad9cc"", ""experimentId"" : ""6384d56b96e8d228551ec182"", ""deploymentId"" : 400000032 } ] } } ===== Log before crash start ===== You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Compositor returned null texture > open 1URJ 1urj title: Single stranded DNA-binding protein(ICP8) from Herpes simplex virus-1 [more info...] Chain information for 1urj #1 --- Chain | Description | UniProt A B | MAJOR DNA-BINDING PROTEIN | DNBI_HSV11 1-1136 Non-standard residues in 1urj #1 --- HG — mercury (II) ion ZN — zinc ion 1urj mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly > ui tool show ""Scale Bar"" > scalebar > scalebar 140 > close > open /Users/pep/Downloads/ChimeraX/AlphaFold/prediction_3/best_model.pdb > format pdb Chain information for best_model.pdb #1 --- Chain | Description A | No description available > close > open /Volumes/SUN-CPR-Kummer-Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb > format pdb No such file/path: /Volumes/SUN-CPR-Kummer- Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb > open /Volumes/SUN-CPR-Kummer-Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb > format pdb No such file/path: /Volumes/SUN-CPR-Kummer- Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb > open /Volumes/SUN-CPR-Kummer-Group/PepCunillSubiranas/AF_UL9/ranked_0.pdb > format pdb Chain information for ranked_0.pdb #1 --- Chain | Description B C | No description available > scalebar 140 > scalebar 124 > color bynucleotide > scalebar off > lighting simple > set bgColor white > lighting soft > lighting flat > lighting full > ui tool show ""Show Sequence Viewer"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > sequence chain /B /C Alignment identifier is 1 > select /B-C:1-2 36 atoms, 36 bonds, 4 residues, 1 model selected > select /B-C:1-534 8350 atoms, 8544 bonds, 1068 residues, 1 model selected > color sel #cc3333ff > color sel #993333ff > color sel #cc3333ff > select clear > select /B-C:535-536 28 atoms, 26 bonds, 4 residues, 1 model selected > select /B-C:535-808 4246 atoms, 4340 bonds, 548 residues, 1 model selected > select > /B-C:19-26,31-35,40-47,85-96,111-123,132-134,143-145,152-157,160-163,174-182,189-202,215-225,227-229,240-243,255-262,277-280,284-293,305-317,334-339,376-384,400-402,416-422,426-447,450-453,457-461,463-474,476-489,505-531,539-544,546-555,562-573,575-592,594-597,600-610,636-651,656-658,667-689,696-699,702-711,722-738,755-757,760-769,780-789,791-794,805-809,815-817,823-831,834-836,846-848 6896 atoms, 6940 bonds, 862 residues, 1 model selected > select clear > select /B-C:535 18 atoms, 16 bonds, 2 residues, 1 model selected > select /B-C:535-849 4856 atoms, 4964 bonds, 630 residues, 1 model selected > color sel #330000ff > color sel #ff0000ff > color sel #ff9966ff > color sel #990000ff > color sel #330000ff > select clear > color #333333ff > undo > select /B-C:535 18 atoms, 16 bonds, 2 residues, 1 model selected > select /B-C:535-849 4856 atoms, 4964 bonds, 630 residues, 1 model selected > color sel #666666ff > select clear > select /B-C:564 18 atoms, 16 bonds, 2 residues, 1 model selected > select /B-C:564-573 160 atoms, 158 bonds, 20 residues, 1 model selected > select /B-C:565 16 atoms, 14 bonds, 2 residues, 1 model selected > select /B-C:565-611 766 atoms, 778 bonds, 94 residues, 1 model selected > select /B-C:564-565 34 atoms, 32 bonds, 4 residues, 1 model selected > select /B-C:564-829 4116 atoms, 4206 bonds, 532 residues, 1 model selected > select /B-C:564 18 atoms, 16 bonds, 2 residues, 1 model selected > select /B-C:564-832 4162 atoms, 4252 bonds, 538 residues, 1 model selected > select clear > select /B 6603 atoms, 6755 bonds, 849 residues, 1 model selected > roll > stop > orient reset Unknown command: orient reset > view orient > select clear > turn 90 Expected an axis vector or a keyword > turn 90x Expected an axis vector or a keyword > turn 90 x Expected an axis vector or a keyword > turn 90 90 Expected an axis vector or a keyword > turn x 90 > turn x -90 > turn x 180 > turn x -180 > ui tool show ""Side View"" > turn z 90 > turn z -90 > turn y 90 > turn 180 Expected an axis vector or a keyword > turn 180 Expected an axis vector or a keyword > turn x 180 > undo > view orient > lighting flat > lighting full > lighting flat > lighting simple > lighting shadows true > lighting shadows false > graphics silhouettes false > graphics silhouettes true > set bgColor gray > set bgColor white > lighting full > lighting simple > show surfaces > lighting soft > lighting simple > lighting full > hide surfaces > show cartoons > surface style dot > show surfaces > select helix 6896 atoms, 6940 bonds, 862 residues, 1 model selected > select strand 1458 atoms, 1442 bonds, 181 residues, 1 model selected > hide sel surfaces > show sel surfaces > hide sel surfaces > show sel surfaces > select 13206 atoms, 13510 bonds, 1698 residues, 1 model selected > hide sel surfaces > select clear > select helix 6896 atoms, 6940 bonds, 862 residues, 1 model selected > select clear > select strand 1458 atoms, 1442 bonds, 181 residues, 1 model selected > select clear > select /B-C:783 16 atoms, 14 bonds, 2 residues, 1 model selected > select /B-C:783-792 168 atoms, 170 bonds, 20 residues, 1 model selected > select /B-C:773 16 atoms, 14 bonds, 2 residues, 1 model selected > select /B-C:773-795 384 atoms, 392 bonds, 46 residues, 1 model selected > select /B-C:766 16 atoms, 14 bonds, 2 residues, 1 model selected > select /B-C:766-795 498 atoms, 510 bonds, 60 residues, 1 model selected > select /B-C:760 18 atoms, 16 bonds, 2 residues, 1 model selected > select /B-C:760-794 576 atoms, 588 bonds, 70 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > save /Users/pep/Desktop/s format fasta alignment 1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select /B-C:1-2 36 atoms, 36 bonds, 4 residues, 1 model selected > select /B-C:1-654 10220 atoms, 10454 bonds, 1308 residues, 1 model selected > select /B-C:66 10 atoms, 8 bonds, 2 residues, 1 model selected > select /B-C:66-231 2588 atoms, 2632 bonds, 332 residues, 1 model selected > select clear > view orient > turn y 90 > save /Users/pep/Desktop/image39.png supersample 3 > turn y -90 > save /Users/pep/Desktop/image40.png supersample 3 > ui tool show ""Color Actions"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > rainbow > view orient > save /Users/pep/Desktop/image41.png supersample 3 > ui tool show ""AlphaFold Error Plot"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Must choose path to predicted aligned file > alphafold pae #1 file /Volumes/SUN-CPR-Kummer- > Group/PepCunillSubiranas/AF_UL9/result_model_5_multimer_v3_pred_0.pkl The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color #1/B:11-547 lime > color #1/B:18-313 lime > color #1/B:550-849/C:1-4 magenta > color #1/B:7-272 lime > color #1/B:279-533 magenta > color #1/B:537-849/C:1-11 lime > color #1/B:537-836 lime > color #1/C:35-258 magenta > color #1/B:533-849 lime > color #1/C:7-282 lime > color #1/C:275-550 lime > color #1/C:4-533 lime > color #1/C:399-399 lime > color #1/C:334-334 magenta > color #1/C:21-533 lime > color #1/C:557-557 lime > color #1/C:269-269 magenta > color #1/C:286-540 lime > color #1/C:516-849 lime > color #1/B:18-843 lime > color #1/C:11-849 lime > color #1/B:14-843 magenta > color #1/B:11-533 lime > color #1/C:21-530 magenta > color #1/B:523-849/C:1-7 lime > color #1/C:14-537 magenta > color #1/B:447-447 lime > color #1/C:337-337 magenta > color #1/B:11-76 lime > color #1/C:21-45 magenta > color #1/B:516-843 lime > color #1/C:11-530 magenta > color #1/B:777-777 lime > color #1/C:296-296 magenta > color #1/C:7-540 lime > color #1/C:513-513 lime > color #1/C:636-636 magenta > color #1/C:4-849 lime > color #1/B:4-846 lime > color #1/B:4-843 lime > color #1/C:7-849 magenta > color #1/C:11-11 lime > color #1/C:705-705 magenta > color #1/B:4-846 lime > color #1/C:11-849 magenta > color #1/C:330-330 lime > color #1/B:674-674 magenta > color #1/C:14-849 lime > color #1/B:4-849 magenta > color #1/C:654-654 lime > color #1/B:757-757 magenta > ui tool show ""ESMFold Error Plot"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Must choose path to predicted aligned file > esmfold pae #1 file /Volumes/SUN-CPR-Kummer- > Group/PepCunillSubiranas/AF_UL9/result_model_5_multimer_v3_pred_0.pkl The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color #1/C:21-303 lime > color #1/C:38-547 lime > color #1/C:14-265 lime > color #1/C:293-293 lime > color #1/C:300-300 magenta > color #1/C:7-605 lime > color #1/C:526-526 lime > color #1/C:379-379 magenta > color #1/C:7-279 lime > color #1/C:540-540 lime > color #1/C:372-375 magenta > color #1/C:25-547 lime > color #1/C:327-327 lime > color #1/C:547-547 magenta > color #1/C:265-537 lime > color #1/C:523-523 lime > color #1/C:585-585 magenta > color #1/C:533-843 lime > color #1/C:471-471 lime > color #1/C:341-341 magenta > color #1/B:21-547 lime > color #1/B:657-657 lime > color #1/B:296-296 magenta > color #1/B:557-832 lime > color #1/B:21-286 magenta > color #1/C:561-561 lime > color #1/B:825-825 magenta > undo > Incomplete command: shape > shape cylinder > select 13206 atoms, 13510 bonds, 1698 residues, 2 models selected > shape cylinder The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > PipesAndPlanks Unknown command: PipesAndPlanks > cartoon style (#!1 & sel & coil) xsection oval > cartoon style (#!1 & sel) xsection barbell modeHelix default > select clear > cartoon style xsection oval modeHelix default > undo > ui tool show ""Basic Actions"" > hide /B target abp > ui tool show ""Render by Attribute"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select clear > undo > view orient > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color bfactor palette > color byattribute bfactor palette Missing ""palette"" keyword's argument > color bfactor palette > color byattribute bfactor palette Missing ""palette"" keyword's argument > color bfactor palette > color byattribute bfactor palette Missing ""palette"" keyword's argument > color bfactor palette > color byattribute bfactor palette Missing ""palette"" keyword's argument > color bfactor palette > color byattribute bfactor palette Missing ""palette"" keyword's argument > color bfactor palette > color byattribute bfactor palette Missing ""palette"" keyword's argument > color bfactor palette > color byattribute bfactor palette Missing ""palette"" keyword's argument > color bfactor palette > color byattribute bfactor palette Missing ""palette"" keyword's argument > color bfactor palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color bfactor palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > view orient > lighting soft > lighting simple > lighting soft > lighting full > undo > ui tool show ""Surface Color"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Color Key"" > ui mousemode right ""color key"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key blue-white-red :min : :max white: The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key blue:min white: red:max white: white: > key white: white: red:max white: blue:min > key blue:min white: red:max white: white: > key white: white: red:max white: blue:min > key white: white: red:max white: blue:1 > key white: white: red:max white: blue:10 > key white: white: red:max white: blue:100 > key white: white: red:max white:9 blue:100 > key white: white: red:max white:90 blue:100 > key white: white: red:7 white:90 blue:100 > key white: white: red:70 white:90 blue:100 > key white: white:5 red:70 white:90 blue:100 > key white: white:50 red:70 white:90 blue:100 > key white:0 white:50 red:70 white:90 blue:100 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key numericLabelSpacing equal > key white:0 white:50 red:70 #f8fffa:90 blue:100 > key white:0 white:50 red:70 #f9fffb:90 blue:100 > key white:0 white:50 red:70 #f8fffb:90 blue:100 > key white:0 white:50 red:70 #f8fffc:90 blue:100 > key white:0 white:50 red:70 #f7fffc:90 blue:100 > key white:0 white:50 red:70 #f6fffc:90 blue:100 > key white:0 white:50 red:70 #f3fffd:90 blue:100 > key white:0 white:50 red:70 #f1fffe:90 blue:100 > key white:0 white:50 red:70 #f0fffe:90 blue:100 > key white:0 white:50 red:70 #eaffff:90 blue:100 > key white:0 white:50 red:70 #e6feff:90 blue:100 > key white:0 white:50 red:70 #dffdff:90 blue:100 > key white:0 white:50 red:70 #d9fbff:90 blue:100 > key white:0 white:50 red:70 #d6faff:90 blue:100 > key white:0 white:50 red:70 #d2f9ff:90 blue:100 > key white:0 white:50 red:70 #cbf7ff:90 blue:100 > key white:0 white:50 red:70 #caf6ff:90 blue:100 > key white:0 white:50 red:70 #c5f5ff:90 blue:100 > key white:0 white:50 red:70 #bff2ff:90 blue:100 > key white:0 white:50 red:70 #bcf1ff:90 blue:100 > key white:0 white:50 red:70 #baf0ff:90 blue:100 > key white:0 white:50 red:70 #b5edff:90 blue:100 > key white:0 white:50 red:70 #b3ecff:90 blue:100 > key white:0 white:50 red:70 #b2ebff:90 blue:100 > key white:0 white:50 red:70 #afeaff:90 blue:100 > key white:0 white:50 red:70 #aee9ff:90 blue:100 > key white:0 white:50 red:70 #ade8ff:90 blue:100 > key white:0 white:50 red:70 #aae6ff:90 blue:100 > key white:0 white:50 red:70 #a9e5ff:90 blue:100 > key white:0 white:50 red:70 #a7e5ff:90 blue:100 > key white:0 white:50 red:70 #a5e3ff:90 blue:100 > key white:0 white:50 red:70 #a5e2ff:90 blue:100 > key white:0 white:50 red:70 #a4e2ff:90 blue:100 > key white:0 white:50 red:70 #a2e1ff:90 blue:100 > key white:0 white:50 red:70 #a1e0ff:90 blue:100 > key white:0 white:50 red:70 #a0e0ff:90 blue:100 > key white:0 white:50 red:70 #a0dfff:90 blue:100 > key white:0 white:50 red:70 #9fdfff:90 blue:100 > key white:0 white:50 red:70 #9dddff:90 blue:100 > key white:0 white:50 red:70 #9bddff:90 blue:100 > key white:0 white:50 red:70 #9bdcff:90 blue:100 > key white:0 white:50 red:70 #9adcff:90 blue:100 > key white:0 white:50 red:70 #9adbff:90 blue:100 > key white:0 white:50 red:70 #99dbff:90 blue:100 > key white:0 white:50 red:70 #97daff:90 blue:100 > key white:0 white:50 red:70 #96d9ff:90 blue:100 > key white:0 white:50 red:70 #95d9ff:90 blue:100 > key white:0 white:50 red:70 #94d8ff:90 blue:100 > key white:0 white:50 red:70 #92d8ff:90 blue:100 > key white:0 white:50 red:70 #91d7ff:90 blue:100 > key white:0 white:50 red:70 #8fd7ff:90 blue:100 > key white:0 white:50 red:70 #8ed6ff:90 blue:100 > key white:0 white:50 red:70 #8dd6ff:90 blue:100 > key white:0 white:50 red:70 #8cd6ff:90 blue:100 > key white:0 white:50 red:70 #8bd5ff:90 blue:100 > key white:0 white:50 red:70 #8ad4ff:90 blue:100 > key white:0 white:50 red:70 #88d4ff:90 blue:100 > key white:0 white:50 red:70 #87d3ff:90 blue:100 > key white:0 white:50 red:70 #85d3ff:90 blue:100 > key white:0 white:50 red:70 #82d2ff:90 blue:100 > key white:0 white:50 red:70 #81d1ff:90 blue:100 > key white:0 white:50 red:70 #80d1ff:90 blue:100 > key white:0 white:50 red:70 #7fd1ff:90 blue:100 > key white:0 white:50 red:70 #7ed0ff:90 blue:100 > key white:0 white:50 red:70 #7ccfff:90 blue:100 > key white:0 white:50 red:70 #7aceff:90 blue:100 > key white:0 white:50 red:70 #79ceff:90 blue:100 > key white:0 white:50 red:70 #79cdff:90 blue:100 > key white:0 white:50 red:70 #78cdff:90 blue:100 > key white:0 white:50 red:70 #77cdff:90 blue:100 > key white:0 white:50 red:70 #76ccff:90 blue:100 > key white:0 white:50 red:70 #76cbff:90 blue:100 > key white:0 white:50 red:70 #75cbff:90 blue:100 > key white:0 white:50 red:70 #74cbff:90 blue:100 > key white:0 white:50 red:70 #74caff:90 blue:100 > key white:0 white:50 red:70 #73caff:90 blue:100 > key white:0 white:50 red:70 #70c8ff:90 blue:100 > key white:0 white:50 red:70 #6fc8ff:90 blue:100 > key white:0 white:50 red:70 #6dc7ff:90 blue:100 > key white:0 white:50 red:70 #69c5ff:90 blue:100 > key white:0 white:50 red:70 #66c4ff:90 blue:100 > key white:0 white:50 red:70 #64c2ff:90 blue:100 > key white:0 white:50 red:70 #63c2ff:90 blue:100 > key white:0 white:50 red:70 #61c1ff:90 blue:100 > key white:0 white:50 red:70 #60c0ff:90 blue:100 > key white:0 white:50 red:70 #5ebfff:90 blue:100 > key white:0 white:50 red:70 #5cbfff:90 blue:100 > key white:0 white:50 red:70 #5bbeff:90 blue:100 > key white:0 white:50 red:70 #5abeff:90 blue:100 > key white:0 white:50 red:70 #58bcff:90 blue:100 > key white:0 white:50 red:70 #57bcff:90 blue:100 > key white:0 white:50 red:70 #56bbff:90 blue:100 > key white:0 white:50 red:70 #55bbff:90 blue:100 > key white:0 white:50 red:70 #53bbff:90 blue:100 > key white:0 white:50 red:70 #51baff:90 blue:100 > key white:0 white:50 red:70 #50b9ff:90 blue:100 > key white:0 white:50 red:70 #4eb8ff:90 blue:100 > key white:0 white:50 red:70 #4cb7ff:90 blue:100 > key white:0 white:50 red:70 #4ab6ff:90 blue:100 > key white:0 white:50 red:70 #48b6ff:90 blue:100 > key white:0 white:50 red:70 #48b5ff:90 blue:100 > key white:0 white:50 red:70 #46b4ff:90 blue:100 > key white:0 white:50 red:70 #44b3ff:90 blue:100 > key white:0 white:50 red:70 #43b2ff:90 blue:100 > key white:0 white:50 red:70 #41b1ff:90 blue:100 > key white:0 white:50 red:70 #3fb0ff:90 blue:100 > key white:0 white:50 red:70 #3caeff:90 blue:100 > key white:0 white:50 red:70 #3cadff:90 blue:100 > key white:0 white:50 red:70 #38abff:90 blue:100 > key white:0 white:50 red:70 #37aaff:90 blue:100 > key white:0 white:50 red:70 #37a9ff:90 blue:100 > key white:0 white:50 red:70 #35a8ff:90 blue:100 > key white:0 white:50 red:70 #32a6ff:90 blue:100 > key white:0 white:50 red:70 #30a4ff:90 blue:100 > key white:0 white:50 red:70 #30a3ff:90 blue:100 > key white:0 white:50 red:70 #2fa3ff:90 blue:100 > key white:0 white:50 red:70 #2ea2ff:90 blue:100 > key white:0 white:50 red:70 #2da1ff:90 blue:100 > key white:0 white:50 red:70 #2ca1ff:90 blue:100 > key white:0 white:50 red:70 #2ca0ff:90 blue:100 > key white:0 white:50 red:70 #2ba0ff:90 blue:100 > key white:0 white:50 red:70 #2b9fff:90 blue:100 > key white:0 white:50 red:70 #2a9fff:90 blue:100 > key white:0 white:50 red:70 #2a9eff:90 blue:100 > key white:0 white:50 red:70 #299eff:90 blue:100 > key white:0 white:50 red:70 #299dff:90 blue:100 > key white:0 white:50 red:70 #289eff:90 blue:100 > key white:0 white:50 red:70 #299dff:90 blue:100 > key white:0 white:50 red:70 #2a9dff:90 blue:100 > key white:0 white:50 red:70 #2b9dff:90 blue:100 > key white:0 white:50 red:70 #2c9eff:90 blue:100 > key white:0 white:50 red:70 #2e9fff:90 blue:100 > key white:0 white:50 red:70 #2fa0ff:90 blue:100 > key white:0 white:50 red:70 #30a0ff:90 blue:100 > key white:0 white:50 red:70 #35a5ff:90 blue:100 > key white:0 white:50 red:70 #37a7ff:90 blue:100 > key white:0 white:50 red:70 #38a8ff:90 blue:100 > key white:0 white:50 red:70 #3cacff:90 blue:100 > key white:0 white:50 red:70 #3dadff:90 blue:100 > key white:0 white:50 red:70 #3daeff:90 blue:100 > key white:0 white:50 red:70 #3fb1ff:90 blue:100 > key white:0 white:50 red:70 #41b4ff:90 blue:100 > key white:0 white:50 red:70 #42b7ff:90 blue:100 > key white:0 white:50 red:70 #43b9ff:90 blue:100 > key white:0 white:50 red:70 #44bcff:90 blue:100 > key white:0 white:50 red:70 #44bdff:90 blue:100 > key white:0 white:50 red:70 #45bfff:90 blue:100 > key white:0 white:50 red:70 #46c1ff:90 blue:100 > key white:0 white:50 red:70 #47c5ff:90 blue:100 > key white:0 white:50 red:70 #48c7ff:90 blue:100 > key white:0 white:50 red:70 #49cbff:90 blue:100 > key white:0 white:50 red:70 #4acdff:90 blue:100 > key white:0 white:50 red:70 #4aceff:90 blue:100 > key white:0 white:50 red:70 #4acfff:90 blue:100 > key white:0 white:50 red:70 #4ad0ff:90 blue:100 > key white:0 white:50 red:70 #4bd1ff:90 blue:100 > key white:0 white:50 red:70 #4bd2ff:90 blue:100 > key white:0 white:50 red:70 #4bd3ff:90 blue:100 > key white:0 white:50 red:70 #4cd4ff:90 blue:100 > key white:0 white:50 red:70 #4cd5ff:90 blue:100 > key white:0 white:50 red:70 #4cd6ff:90 blue:100 > key white:0 white:50 red:70 #4dd7ff:90 blue:100 > key white:0 white:50 red:70 #4dd8ff:90 blue:100 > key white:0 white:50 red:70 #4ed9ff:90 blue:100 > key white:0 white:50 red:70 #4dd9ff:90 blue:100 > key white:0 white:50 red:70 #4cdaff:90 blue:100 > key white:0 white:50 red:70 #4cdbff:90 blue:100 > key white:0 white:50 red:70 #4cdcff:90 blue:100 > key white:0 white:50 red:70 #4bddff:90 blue:100 > key white:0 white:50 red:70 #4adeff:90 blue:100 > key white:0 white:50 red:70 #4adfff:90 blue:100 > key white:0 white:50 red:70 #49dfff:90 blue:100 > key white:0 white:50 red:70 #48dfff:90 blue:100 > key white:0 white:50 red:70 #47e0ff:90 blue:100 > key white:0 white:50 red:70 #46e0ff:90 blue:100 > color key alphafold Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > 2dlabels > key labelColor #bfbfbf > key labelColor default > key fontSize 23 > key fontSize 22 > key fontSize 21 > key fontSize 20 > key fontSize 21 > key fontSize 22 > key fontSize 23 > key fontSize 24 > key fontSize 25 > key fontSize 26 > key fontSize 27 > key fontSize 28 > key fontSize 29 > key fontSize 30 > key fontSize 31 > key fontSize 32 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key alphafold :0 :50 :70 :90 :100 > key pos 0.768809,0.116257 size 0.00882056,0.0013392 > key pos 0.782114,0.06833 size 0.204062,0.123147 > key pos 0.698122,0.0823282 size 0,0 > key pos 0.658725,0.1046 size 0.313036,0.0376553 > undo > key pos 0.604018,0.0666726 > key fontSize 31 > key pos 0.636059,0.102636 size 0.27705,0.0392079 > key paecontacts :100 :90 :70 :50 :0 > key alphafold :0 :50 :70 :90 :100 > undo > key pos 0.637544,0.0996112 > ui mousemode right translate > ui mousemode left 'color key' > ui mousemode left rotate > ui mousemode right 'color key' > help help:user/tools/colorkey.html The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > 2dlabels text ""pLDDT values"" > key pos 0.168664,0.471023 size 0.361155,0.0398326 > key pos 0.539279,0.0803392 > key pos 0.527306,0.435428 size 0.00759199,0.0740672 > undo > key pos 0.656943,0.0565185 size 0.273768,0.0225437 > key pos 0.548738,0.430832 size 0.2568,0.077924 > key pos 0.575605,0.0834756 size 0.360068,0.0221138 > ui mousemode right translate > ui mousemode right ""move label"" > 2dlabels #6.1 xpos 0.579 ypos 0.120 > 2dlabels #6.1 xpos 0.672 ypos 0.175 > ui mousemode right ""color key"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key pos 0.591624,0.141009 size 0.152361,0.0260973 > key pos 0.56595,0.0847163 > ui mousemode right ""move label"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui mousemode right ""move label"" > 2dlabels #6.2 xpos 1.231 ypos 0.363 > 2dlabels #6.1 xpos 0.566 ypos 0.120 > view orient > hide cartoons > show cartoons > color bfactor #1 palette esmfold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color bfactor #1 palette esmfold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color bfactor #1 palette esmfold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > save /Users/pep/Desktop/image42.png supersample 3 > turn x 90 > turn y 90 > save /Users/pep/Desktop/image43.png supersample 3 > alphafold pae #1 colorDomains true > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > select /B-C:231-232 34 atoms, 34 bonds, 4 residues, 1 model selected > select /B-C:1-232 3586 atoms, 3658 bonds, 464 residues, 1 model selected > select /B 6603 atoms, 6755 bonds, 849 residues, 1 model selected > view orient > turn y 90 > axis Unknown command: axis > select clear > select /B-C:1 22 atoms, 22 bonds, 2 residues, 1 model selected > select /B-C:1-19 248 atoms, 252 bonds, 38 residues, 1 model selected > select /B-C:544 18 atoms, 16 bonds, 2 residues, 1 model selected > select /B-C:544-549 90 atoms, 88 bonds, 12 residues, 1 model selected > select > /B-C:19-26,31-35,40-47,85-96,111-123,132-134,143-145,152-157,160-163,174-182,189-202,215-225,227-229,240-243,255-262,277-280,284-293,305-317,334-339,376-384,400-402,416-422,426-447,450-453,457-461,463-474,476-489,505-531,539-544,546-555,562-573,575-592,594-597,600-610,636-651,656-658,667-689,696-699,702-711,722-738,755-757,760-769,780-789,791-794,805-809,815-817,823-831,834-836,846-848 6896 atoms, 6940 bonds, 862 residues, 1 model selected > select clear > select /B-C:544 18 atoms, 16 bonds, 2 residues, 1 model selected > select /B-C:539-544 80 atoms, 80 bonds, 12 residues, 1 model selected The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > select /B-C:623 18 atoms, 16 bonds, 2 residues, 1 model selected > select /B-C:623-629 108 atoms, 106 bonds, 14 residues, 1 model selected > select /B-C:539 14 atoms, 14 bonds, 2 residues, 1 model selected > select /B-C:539-544 80 atoms, 80 bonds, 12 residues, 1 model selected > select /B-C:539-544,624-629 170 atoms, 168 bonds, 24 residues, 1 model selected > show sel atoms > select clear > undo > color (#!1 & sel) red > select clear > select /B 6603 atoms, 6755 bonds, 849 residues, 1 model selected > select clear > color bfactor 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Already setting window visible! > alphafold pae #1 colorDomains true The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color bfactor #1 palette esmfold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color bfactor #1 palette esmfold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. Already setting window visible! The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > help help:user/tools/alphafold.html#pae The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color #1/B:1-1 lime > color #1/B:3-849/C:1-849 lime The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > help help:user/tools/alphafold.html#pae > axiscolor plot alphafold Unknown command: axiscolor plot alphafold > color plot alphafold Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Color Actions"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > ui tool show ""Color Actions"" > key pae :0 : : :15 : : :30 showTool true > alphafold pae #1 colorDomains true > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > ui tool show ""Side View"" > key paegreen :0 : : :15 : : :30 showTool true The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color paegreen Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > key red:low orange: yellow: cornflowerblue: blue:high > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 Already setting window visible! > select > /B-C:19-26,31-35,40-47,85-96,111-123,132-134,143-145,152-157,160-163,174-182,189-202,215-225,227-229,240-243,255-262,277-280,284-293,305-317,334-339,376-384,400-402,416-422,426-447,450-453,457-461,463-474,476-489,505-531,539-544,546-555,562-573,575-592,594-597,600-610,636-651,656-658,667-689,696-699,702-711,722-738,755-757,760-769,780-789,791-794,805-809,815-817,823-831,834-836,846-848 6896 atoms, 6940 bonds, 862 residues, 1 model selected > color bfactor #1 palette paegreen 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > select clear The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key paegreen :0 : : :15 : : :30 showTool true > ui mousemode right ""color key"" The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key pos 0.604378,0.134006 size 0.100855,0.0970887 > key pos 0.820187,0.123753 size 0.125421,0.0236736 > key pos 0.852465,0.226314 size 0.0136468,0.46242 > key pos 0.71884,0.101136 size 0.0230012,0.286266 > key pos 0.707525,0.0439381 size 0.241037,0.0149871 > save /Users/pep/Desktop/image44.png supersample 3 > key pos 0.14223,0.658284 size 0.279099,0.0285492 > save /Users/pep/Desktop/image45.png supersample 3 The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color #1/C:524-524 lime > color #1/C:594-594 magenta The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > color #1/C:630-630 lime > color #1/B:671-671 magenta > alphafold pae #1 colorDomains true The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > key pos 0.757436,0.542016 size 0.0591203,0.0337354 > key pos 0.327701,0.687724 size 0,0 Already setting window visible! > color #1/C:690-690 lime > color #1/C:152-152 magenta > color #1/C:557-557 lime > color #1/B:254-254 magenta The cached device pixel ratio value was stale on window expose. Please file a QTBUG which explains how to reproduce. > alphafold pae #1 colorDomains true > lighting simple > lighting flat > lighting simple > lighting shadows true > lighting shadows false > lighting flat > graphics silhouettes false > lighting soft > lighting full > lighting flat > lighting simple > graphics silhouettes false > color #1/C:636-636 lime > color #1/C:284-284 magenta > color bfactor #1 palette alphafold 13206 atoms, 1698 residues, 2 surfaces, atom bfactor range 16.4 to 98.1 > key pos 0.424738,0.596559 size 0.0251048,0.0302724 > key pos 0.722385,0.526184 size 0.204108,0.121798 > key pos 0.910091,0.424162 size 0,0 > key pos 0.56261,0.102205 size 0.305485,0.0158445 > key pos 0.244068,0.094711 size 0.446295,0.0456157 > key pos 0.23177,0.0820312 size 0.437232,0.042045 > key pos 0.228959,0.0748773 > key alphafold :0 : : :50 : : :70 : : :90:::100 showTool true Expected a keyword > key alphafold :0 : : :50 : : :70 : : :90:::100 showTool true Expected a keyword > key alphafold :0 : : :50 : : :70 : : :90:::100 showTool true Expected a keyword > key red:low orange: yellow: cornflowerblue: blue:high > ui tool show ""Color Key"" > key alphafold :low : : : :1 > key alphafold :low : : : :10 > key alphafold :low : : : :100 > key alphafold :low : : :9 :100 > key alphafold :low : : :90 :100 > key alphafold :low : :7 :90 :100 > key alphafold :low : :70 :90 :100 > key alphafold :low :5 :70 :90 :100 > key alphafold :low :50 :70 :90 :100 > key alphafold :0 :50 :70 :90 :100 > ui mousemode right ""move label"" > close #4 > close #3 > view orient > select 13206 atoms, 13510 bonds, 1698 residues, 5 models selected > hide sel atoms > select clear > save /Users/pep/Desktop/image46.png supersample 3 ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.8.dev202403220040 (2024-03-22) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.6.1, Qt 6.6.1 Qt runtime version: 6.6.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: Z15G0007QDK/A Chip: Apple M1 Pro Total Number of Cores: 8 (6 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.101.3 OS Loader Version: 10151.101.3 Software: System Software Overview: System Version: macOS 14.4.1 (23E224) Kernel Version: Darwin 23.4.0 Time since boot: 1 day, 17 hours, 11 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 14 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal LEN T27q-20: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 Babel: 2.14.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.0.0 build: 1.1.1 certifi: 2023.11.17 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.16 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.3 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.5 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.56 ChimeraX-AtomicLibrary: 14.0.2 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.12.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.8.dev202403220040 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 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: 1.1.9 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.3 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.15 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: 1.1 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.3 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: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.3 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: 1.0 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: 1.16.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2 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: 1.37.1 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 3.0.9 debugpy: 1.8.1 decorator: 5.1.1 docutils: 0.20.1 executing: 2.0.1 filelock: 3.13.1 fonttools: 4.50.0 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.10.0 html2text: 2024.2.26 idna: 3.6 ihm: 0.43 imagecodecs: 2024.1.1 imagesize: 1.4.1 ipykernel: 6.29.2 ipython: 8.21.0 ipywidgets: 8.1.2 jedi: 0.19.1 Jinja2: 3.1.3 jupyter-client: 8.6.0 jupyter-core: 5.7.2 jupyterlab-widgets: 3.0.10 kiwisolver: 1.4.5 line-profiler: 4.1.2 lxml: 5.1.0 lz4: 4.3.3 MarkupSafe: 2.1.5 matplotlib: 3.8.3 matplotlib-inline: 0.1.6 msgpack: 1.0.8 ndindex: 1.8 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.2.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.9.0 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.3 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.2.0 pip: 24.0 pkginfo: 1.10.0 platformdirs: 4.2.0 prompt-toolkit: 3.0.43 psutil: 5.9.8 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.3.0 pygments: 2.17.2 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3302 pyparsing: 3.1.2 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.6.1 PyQt6-Qt6: 6.6.2 PyQt6-sip: 13.6.0 PyQt6-WebEngine-commercial: 6.6.0 PyQt6-WebEngine-Qt6: 6.6.2 python-dateutil: 2.9.0.post0 pytz: 2024.1 pyzmq: 25.1.2 qtconsole: 5.5.1 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.12.0 setuptools: 69.2.0 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: 2.0.0 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: 0.6.1 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2024.1.30 tinyarray: 1.2.4 tornado: 6.4 traitlets: 5.14.1 typing-extensions: 4.10.0 tzdata: 2024.1 urllib3: 2.2.1 wcwidth: 0.2.13 webcolors: 1.13 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.10 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX