id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6897 Graphics driver crash, macOS 12.3.1, Radeon RX Vega 64 shweta.bhatt@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-10.16-x86_64-i386-64bit ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. I asked CHIMERAX to use external GPU and then it was not working. Fatal Python error: Aborted Current thread 0x0000000116d28600 (most recent call first): File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/OpenGL/GL/VERSION/GL_1_5.py"", line 125 in glBufferSubData File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/opengl.py"", line 1626 in set_multishadow_view File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 227 in _draw_scene File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/graphics/view.py"", line 165 in draw File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 73 in draw_new_frame File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/updateloop.py"", line 139 in _redraw_timer_callback File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/ui/gui.py"", line 301 in event_loop File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 867 in init File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/ChimeraX_main.py"", line 1018 in File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/runpy.py"", 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""AppKit"", ""CFBundleVersion"" : ""2113.40.127"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4652883968, ""size"" : 5705728, ""uuid"" : ""c723812a-f7a5-3001-98d5-e60e8daa6ffb"", ""path"" : ""\/private\/var\/folders\/*\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/lib\/QtCore.framework\/Versions\/5\/QtCore"", ""name"" : ""QtCore"" }, { ""source"" : ""P"", ""arch"" : ""x86_64"", ""base"" : 4665765888, ""size"" : 4485120, ""uuid"" : ""b432d666-dcab-320a-8496-78a67f554c0e"", ""path"" : ""\/private\/var\/folders\/*\/ChimeraX-1.3.app\/Contents\/Library\/Frameworks\/Python.framework\/Versions\/3.9\/lib\/python3.9\/site-packages\/PyQt5\/Qt\/lib\/QtWidgets.framework\/Versions\/5\/QtWidgets"", ""name"" : ""QtWidgets"" } ], ""sharedCache"" : { ""base"" : 140703451144192, ""size"" : 15224815616, ""uuid"" : ""6cc5ecdc-5119-37f0-9a85-4f48a50f5f78"" }, ""vmSummary"" : ""ReadOnly portion of Libraries: Total=1.5G resident=0K(0%) swapped_out_or_unallocated=1.5G(100%)\nWritable regions: Total=26.5G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=26.5G(100%)\n\n VIRTUAL REGION \nREGION TYPE SIZE COUNT (non-coalesced) \n=========== ======= ======= \nAccelerate framework 1536K 12 \nActivity Tracing 256K 1 \nCG backing stores 3120K 8 \nCG image 304K 57 \nColorSync 244K 29 \nCoreAnimation 2088K 140 \nCoreGraphics 16K 3 \nCoreUI image data 4092K 51 \nFoundation 36K 2 \nKernel Alloc Once 8K 1 \nMALLOC 23.8G 1045 \nMALLOC guard page 32K 8 \nMALLOC_LARGE (reserved) 561.7M 2 reserved VM address space (unallocated)\nMach message 24K 2 \nOpenGL GLSL 384K 5 \nSTACK GUARD 88K 22 \nStack 131.7M 23 \nStack Guard 56.0M 1 \nVM_ALLOCATE 2.0G 150 \n__DATA 42.7M 683 \n__DATA_CONST 32.8M 346 \n__DATA_DIRTY 1660K 217 \n__FONT_DATA 4K 1 \n__GLSLBUILTINS 5176K 1 \n__LINKEDIT 743.9M 145 \n__OBJC_RO 82.6M 1 \n__OBJC_RW 3200K 2 \n__TEXT 770.4M 676 \n__UNICODE 592K 1 \ndyld private memory 1024K 1 \nmapped file 509.2M 66 \nshared memory 2976K 24 \n=========== ======= ======= \nTOTAL 28.7G 3726 \nTOTAL, minus reserved VM space 28.2G 3726 \n"", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""5ffde50ce2aacd000d47a95f"", ""factorPackIds"" : { }, ""deploymentId"" : 240000145 }, { ""rolloutId"" : ""6112e14f37f5d11121dcd519"", ""factorPackIds"" : { ""SIRI_TEXT_TO_SPEECH"" : ""6267122541fbd3022330c3ea"" }, ""deploymentId"" : 240000112 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/N4_fullcapsid/N4_fullcapsid_coot/domain_alignment/gp56-gp17-coot-101.pdb Summary of feedback from opening /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/N4_fullcapsid/N4_fullcapsid_coot/domain_alignment/gp56-gp17-coot-101.pdb --- warnings | Duplicate atom serial number found: 12179 Duplicate atom serial number found: 12180 Duplicate atom serial number found: 12181 Duplicate atom serial number found: 12182 Duplicate atom serial number found: 12183 24250 messages similar to the above omitted Start residue of secondary structure not found: SHEET 62 6262 ALA J 3 PHE J 8 0 Start residue of secondary structure not found: SHEET 63 6363 THR J 15 ASP J 18 0 Start residue of secondary structure not found: SHEET 64 6464 ALA J 33 HIS J 35 0 End residue of secondary structure not found: SHEET 68 6868 VAL J 271 ALA J 275 0 Chain information for gp56-gp17-coot-101.pdb #1 --- Chain | Description A B C D E F H I | No description available G | No description available J | No description available K | No description available L | No description available > ui tool show Registration Thank you for registering your copy of ChimeraX. By providing the information requested you will be helping us document the impact this software is having in the scientific community. The information you supplied will only be used for reporting summary usage statistics; no individual data will be released. shweta.bhatt@cpr.ku.dk is subscribed to the ChimeraX announcements list > set bgColor white > save /Users/mvc581/Desktop/image12.png supersample 3 > open > /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/N4_fullcapsid/N4_fullcapsid_coot/domain_alignment/gp56-gp17-coot-101.pdb Summary of feedback from opening /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/N4_fullcapsid/N4_fullcapsid_coot/domain_alignment/gp56-gp17-coot-101.pdb --- warnings | Duplicate atom serial number found: 12179 Duplicate atom serial number found: 12180 Duplicate atom serial number found: 12181 Duplicate atom serial number found: 12182 Duplicate atom serial number found: 12183 24250 messages similar to the above omitted Start residue of secondary structure not found: SHEET 62 6262 ALA J 3 PHE J 8 0 Start residue of secondary structure not found: SHEET 63 6363 THR J 15 ASP J 18 0 Start residue of secondary structure not found: SHEET 64 6464 ALA J 33 HIS J 35 0 End residue of secondary structure not found: SHEET 68 6868 VAL J 271 ALA J 275 0 Chain information for gp56-gp17-coot-101.pdb #2 --- Chain | Description A B C D E F H I | No description available G | No description available J | No description available K | No description available L | No description available > close #2 > open > /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/maps/Fullcapsid/FP_job403_700_300.mrc Opened FP_job403_700_300.mrc as #2, grid size 401,401,401, pixel 1.11, shown at level 0.0294, step 2, values float32 > open > /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/maps/Fullcapsid/gp17_FP_700_300.mrc Opened gp17_FP_700_300.mrc as #3, grid size 401,401,401, pixel 1.11, shown at level 3.63e-06, step 2, values float32 > open > /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/TAYLOR_LAB_SBMM/N4/N4_capsid_modelbuilding/maps/Fullcapsid/FP_700_300_blur20.mrc Opened FP_700_300_blur20.mrc as #4, grid size 540,540,540, pixel 0.823, shown at level 0.0266, step 4, values float32 > close #3 > volume #4 step 1 > style stick Changed 33148 atom styles > style ball Changed 33148 atom styles > volume #4 color #0433ff > show cartoons > hide atoms > volume #4 color #0433ff86 > volume #4 color #0433ff54 > volume #4 color black > volume #4 color #d6d6d6 > volume #4 color #0433ff > volume #4 color #0433ff2c > volume #4 color #0433ff2b > undo > redo > style sphere Changed 33148 atom styles > ui tool show Log > save /Users/mvc581/Desktop/image13.png supersample 3 > volume #4 color #fffb00 > volume #4 color #fffb003c > volume #4 color #fffb002c > volume #4 color #fffb002b > color bychain > volume #4 color #ffd479 > volume #4 color #ffd4792a > volume #4 color #ffd4793a > volume #4 color #ffd4793b > volume #4 color #00fdff > volume #4 color #00fdff1b > volume #4 color #d6d6d6 > volume #4 color #fffc79 > volume #4 color #fffb00 > volume #4 color #fffb001e > save /Users/mvc581/Desktop/image14.png supersample 3 > save /Users/mvc581/Desktop/image15.png supersample 3 > volume #4 color #76d6ff > volume #4 color #76d6ff94 > volume #4 color #76d6ff6d > volume #4 color #76d6ff41 > volume #4 color #76d6ff2e > style ball Changed 33148 atom styles > volume #4 color #212121 > volume #4 color #2121215e > volume #4 color #21212125 > volume #4 color #21212120 > volume #4 color #2121211d > save /Users/mvc581/Desktop/image10.png supersample 3 > select /A 3048 atoms, 3107 bonds, 401 residues, 1 model selected > color sel forest green > color sel blue > select /B 3048 atoms, 3107 bonds, 401 residues, 1 model selected > color sel blue > select /C 3048 atoms, 3107 bonds, 401 residues, 1 model selected > color sel blue > select /D 3048 atoms, 3107 bonds, 401 residues, 1 model selected > color sel blue > select /E 3048 atoms, 3107 bonds, 401 residues, 1 model selected > color sel blue > select /E 3048 atoms, 3107 bonds, 401 residues, 1 model selected > select /F 3048 atoms, 3107 bonds, 401 residues, 1 model selected > color sel blue > select /G 2919 atoms, 2977 bonds, 1 pseudobond, 383 residues, 2 models selected > color (#!1 & sel) blue > select /H 3048 atoms, 3107 bonds, 401 residues, 1 model selected > color sel blue > select /I 3048 atoms, 3107 bonds, 401 residues, 1 model selected > color sel blue > select /I 3048 atoms, 3107 bonds, 401 residues, 1 model selected > select /J 2052 atoms, 2089 bonds, 279 residues, 1 model selected > color sel orange red > select /J 2052 atoms, 2089 bonds, 279 residues, 1 model selected > select /K 1902 atoms, 1933 bonds, 277 residues, 1 model selected > color sel orange red > select /L 1891 atoms, 1921 bonds, 1 pseudobond, 275 residues, 2 models selected > color (#!1 & sel) orange red > select clear > save /Users/mvc581/Desktop/image10.png supersample 3 > save /Users/mvc581/Desktop/image11.png supersample 3 > ui tool show ""Model Panel"" > show #!4 models > hide #!4 models > show #!2 models > close #2 > show #!4 models > hide #!4 models > hide #!1 models > open > /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/FROM_COMPUTEROME/N4-FP_capsid/FP- > job740_postprocess_masked.mrc Opened FP-job740_postprocess_masked.mrc as #2, grid size 1350,1350,1350, pixel 1.11, shown at step 1, values float32 > volume #2 region 0,0,0,1349,1349,1349 step 8 > volume #2 step 1 /private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/map/volume_viewer.py:2746: RuntimeWarning: invalid value encountered in log h.show_data(log(counts + 1)) > lighting soft > save > /Users/mvc581/Downloads/WORK_RELATED_FOLDERS/FROM_COMPUTEROME/N4_capsids_pdbs.cxs > includeMaps true Traceback (most recent call last): File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 890, in save session.save(output, version=version, include_maps=include_maps) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 624, in save fserialize(stream, data) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/serialize.py"", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File ""msgpack/_packer.pyx"", line 292, in msgpack._cmsgpack.Packer.pack File ""msgpack/_packer.pyx"", line 298, in msgpack._cmsgpack.Packer.pack File ""msgpack/_packer.pyx"", line 295, in msgpack._cmsgpack.Packer.pack File ""msgpack/_packer.pyx"", line 231, in msgpack._cmsgpack.Packer._pack File ""msgpack/_packer.pyx"", line 202, in msgpack._cmsgpack.Packer._pack ValueError: bytes object is too large ValueError: bytes object is too large File ""msgpack/_packer.pyx"", line 202, in msgpack._cmsgpack.Packer._pack See log for complete Python traceback. Traceback (most recent call last): File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 116, in lambda *args, ses=session: show_save_file_dialog(ses), tool_tip=""Save output file"", File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 127, in show_save_file_dialog _dlg.display(session, **kw) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/dialog.py"", line 51, in display run(session, cmd) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/run.py"", line 36, in run results = command.run(text, log=log, return_json=return_json) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 75, in cmd_save Command(session, registry=registry).run(provider_cmd_text, log=log) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/commands/cli.py"", line 2856, in run result = ci.function(session, **kw_args) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/save_command/cmd.py"", line 89, in provider_save saver_info.save(session, path, **provider_kw) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core_formats/__init__.py"", line 84, in save return cxs_save(session, path, **kw) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 890, in save session.save(output, version=version, include_maps=include_maps) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/session.py"", line 624, in save fserialize(stream, data) File ""/private/var/folders/c1/xvt1_mqn6tn690s8mq3tq33c0000gp/T/AppTranslocation/6A480223-B751-4E8E-8CE2-EB21552EDD32/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/core/serialize.py"", line 65, in msgpack_serialize stream.write(packer.pack(obj)) File ""msgpack/_packer.pyx"", line 292, in msgpack._cmsgpack.Packer.pack File ""msgpack/_packer.pyx"", line 298, in msgpack._cmsgpack.Packer.pack File ""msgpack/_packer.pyx"", line 295, in msgpack._cmsgpack.Packer.pack File ""msgpack/_packer.pyx"", line 231, in msgpack._cmsgpack.Packer._pack File ""msgpack/_packer.pyx"", line 202, in msgpack._cmsgpack.Packer._pack ValueError: bytes object is too large ValueError: bytes object is too large File ""msgpack/_packer.pyx"", line 202, in msgpack._cmsgpack.Packer._pack See log for complete Python traceback. ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.3 (2021-12-08) © 2016-2021 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/statusbar.py"", line 84, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/statusbar.py"", line 150, in status r.draw_background() File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 1166, in draw_background GL.glClear(flags) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/OpenGL/platform/baseplatform.py"", line 415, in __call__ return self( *args, **named ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/statusbar.py"", line 84, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/statusbar.py"", line 150, in status r.draw_background() File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 1166, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. Traceback (most recent call last): File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/statusbar.py"", line 84, in _expose_event self.status(self._last_message, self._last_color) File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/ui/statusbar.py"", line 150, in status r.draw_background() File ""/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site- packages/chimerax/graphics/opengl.py"", line 1166, in draw_background GL.glClear(flags) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) OpenGL.error.GLError: GLError( err = 1286, description = b'invalid framebuffer operation', baseOperation = glClear, cArguments = (16640,) ) File ""src/errorchecker.pyx"", line 58, in OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError See log for complete Python traceback. OpenGL version: 4.1 ATI-4.8.15 OpenGL renderer: AMD Radeon RX Vega 64 OpenGL Engine OpenGL vendor: ATI Technologies Inc.Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir8,1 Processor Name: Dual-Core Intel Core i5 Processor Speed: 1,6 GHz Number of Processors: 1 Total Number of Cores: 2 L2 Cache (per Core): 256 KB L3 Cache: 4 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 1731.100.130.0.0 (iBridge: 19.16.14243.0.0,0) OS Loader Version: 540.100.7~23 Software: System Software Overview: System Version: macOS 12.3.1 (21E258) Kernel Version: Darwin 21.4.0 Time since boot: 8 days 19:30 Graphics/Displays: Intel UHD Graphics 617: Chipset Model: Intel UHD Graphics 617 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x87c0 Revision ID: 0x0002 Metal Family: Supported, Metal GPUFamily macOS 2 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 24-Bit Color (ARGB8888) Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal DELL U2719D: Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition) UI Looks like: 2560 x 1440 @ 60.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: 9QF45R2 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: Apple USB-C Digital AV Adapter Adapter Firmware Version: 2,35 AMD Radeon RX Vega 64: Chipset Model: AMD Radeon RX Vega 64 Type: External GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x687f Revision ID: 0x00c1 Metal Family: Supported, Metal GPUFamily macOS 2 GPU is Removable: Yes Locale: (None, 'UTF-8') PyQt5 5.15.2, Qt 5.15.2 Installed Packages: alabaster: 0.7.12 appdirs: 1.4.4 appnope: 0.1.2 Babel: 2.9.1 backcall: 0.2.0 blockdiag: 2.0.1 certifi: 2021.5.30 cftime: 1.5.1.1 charset-normalizer: 2.0.9 ChimeraX-AddCharge: 1.2.2 ChimeraX-AddH: 2.1.11 ChimeraX-AlignmentAlgorithms: 2.0 ChimeraX-AlignmentHdrs: 3.2 ChimeraX-AlignmentMatrices: 2.0 ChimeraX-Alignments: 2.2.3 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.0.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.0 ChimeraX-Atomic: 1.31 ChimeraX-AtomicLibrary: 4.2 ChimeraX-AtomSearch: 2.0 ChimeraX-AtomSearchLibrary: 1.0 ChimeraX-AxesPlanes: 2.0 ChimeraX-BasicActions: 1.1 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.0 ChimeraX-BondRot: 2.0 ChimeraX-BugReporter: 1.0 ChimeraX-BuildStructure: 2.6.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.1 ChimeraX-ButtonPanel: 1.0 ChimeraX-CageBuilder: 1.0 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.2 ChimeraX-ChemGroup: 2.0 ChimeraX-Clashes: 2.2.2 ChimeraX-ColorActions: 1.0 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5 ChimeraX-CommandLine: 1.1.5 ChimeraX-ConnectStructure: 2.0 ChimeraX-Contacts: 1.0 ChimeraX-Core: 1.3 ChimeraX-CoreFormats: 1.1 ChimeraX-coulombic: 1.3.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0 ChimeraX-DataFormats: 1.2.2 ChimeraX-Dicom: 1.0 ChimeraX-DistMonitor: 1.1.5 ChimeraX-DistUI: 1.0 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ExperimentalCommands: 1.0 ChimeraX-FileHistory: 1.0 ChimeraX-FunctionKey: 1.0 ChimeraX-Geometry: 1.1 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1 ChimeraX-Hbonds: 2.1.2 ChimeraX-Help: 1.2 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 ChimeraX-Label: 1.1 ChimeraX-ListInfo: 1.1.1 ChimeraX-Log: 1.1.4 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.8.1 ChimeraX-Map: 1.1 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0 ChimeraX-MapFilter: 2.0 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1 ChimeraX-Markers: 1.0 ChimeraX-Mask: 1.0 ChimeraX-MatchMaker: 2.0.4 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.1 ChimeraX-Meeting: 1.0 ChimeraX-MLP: 1.1 ChimeraX-mmCIF: 2.4 ChimeraX-MMTF: 2.1 ChimeraX-Modeller: 1.2.6 ChimeraX-ModelPanel: 1.2.1 ChimeraX-ModelSeries: 1.0 ChimeraX-Mol2: 2.0 ChimeraX-Morph: 1.0 ChimeraX-MouseModes: 1.1 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nucleotides: 2.0.2 ChimeraX-OpenCommand: 1.7 ChimeraX-PDB: 2.6.5 ChimeraX-PDBBio: 1.0 ChimeraX-PDBLibrary: 1.0.2 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.0.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1 ChimeraX-RemoteControl: 1.0 ChimeraX-ResidueFit: 1.0 ChimeraX-RestServer: 1.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 2.0.1 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.4.6 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0 ChimeraX-Shortcuts: 1.1 ChimeraX-ShowAttr: 1.0 ChimeraX-ShowSequences: 1.0 ChimeraX-SideView: 1.0 ChimeraX-Smiles: 2.1 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.6.1 ChimeraX-STL: 1.0 ChimeraX-Storm: 1.0 ChimeraX-Struts: 1.0 ChimeraX-Surface: 1.0 ChimeraX-SwapAA: 2.0 ChimeraX-SwapRes: 2.1 ChimeraX-TapeMeasure: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1 ChimeraX-ToolshedUtils: 1.2 ChimeraX-Tug: 1.0 ChimeraX-UI: 1.13.7 ChimeraX-uniprot: 2.2 ChimeraX-UnitCell: 1.0 ChimeraX-ViewDockX: 1.0.1 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0 ChimeraX-WebServices: 1.0 ChimeraX-Zone: 1.0 colorama: 0.4.4 cxservices: 1.1 cycler: 0.11.0 Cython: 0.29.24 decorator: 5.1.0 docutils: 0.17.1 filelock: 3.0.12 funcparserlib: 0.3.6 grako: 3.16.5 h5py: 3.6.0 html2text: 2020.1.16 idna: 3.3 ihm: 0.21 imagecodecs: 2021.4.28 imagesize: 1.3.0 ipykernel: 5.5.5 ipython: 7.23.1 ipython-genutils: 0.2.0 jedi: 0.18.0 Jinja2: 3.0.1 jupyter-client: 6.1.12 jupyter-core: 4.9.1 kiwisolver: 1.3.2 lxml: 4.6.3 lz4: 3.1.3 MarkupSafe: 2.0.1 matplotlib: 3.4.3 matplotlib-inline: 0.1.3 msgpack: 1.0.2 netCDF4: 1.5.7 networkx: 2.6.3 numexpr: 2.8.0 numpy: 1.21.2 openvr: 1.16.801 packaging: 21.0 ParmEd: 3.2.0 parso: 0.8.3 pexpect: 4.8.0 pickleshare: 0.7.5 Pillow: 8.3.2 pip: 21.2.4 pkginfo: 1.7.1 prompt-toolkit: 3.0.23 psutil: 5.8.0 ptyprocess: 0.7.0 pycollada: 0.7.1 pydicom: 2.1.2 Pygments: 2.10.0 PyOpenGL: 3.1.5 PyOpenGL-accelerate: 3.1.5 pyparsing: 3.0.6 PyQt5-commercial: 5.15.2 PyQt5-sip: 12.8.1 PyQtWebEngine-commercial: 5.15.2 python-dateutil: 2.8.2 pytz: 2021.3 pyzmq: 22.3.0 qtconsole: 5.1.1 QtPy: 1.11.3 RandomWords: 0.3.0 requests: 2.26.0 scipy: 1.7.1 setuptools: 57.5.0 sfftk-rw: 0.7.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 Sphinx: 4.2.0 sphinx-autodoc-typehints: 1.12.0 sphinxcontrib-applehelp: 1.0.2 sphinxcontrib-blockdiag: 2.0.0 sphinxcontrib-devhelp: 1.0.2 sphinxcontrib-htmlhelp: 2.0.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.3 sphinxcontrib-serializinghtml: 1.1.5 suds-jurko: 0.6 tifffile: 2021.4.8 tinyarray: 1.2.3 tornado: 6.1 traitlets: 5.1.1 urllib3: 1.26.7 wcwidth: 0.2.5 webcolors: 1.11.1 wheel: 0.37.0 wheel-filename: 1.3.0 }}} " defect closed normal Graphics nonchimerax all ChimeraX