id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16260 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.0-x86_64-i386-64bit ChimeraX Version: 1.9rc202410310525 (2024-10-31 05:25:41 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Current thread 0x00007ff85b9c6680 (most recent call first): File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 315 in event_loop File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1003 in init File ""/Applications/ChimeraX-1.8.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1166 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, 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All rights reserved. How to cite UCSF ChimeraX > open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 95 messages similar to the above omitted Chain information for c34_job27_ILS-coot-41.pdb #1 --- Chain | Description 0 | No description available 2 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ci | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available P | No description available R | No description available S | No description available T | No description available U | No description available W | No description available Y | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available > open /Users/lijuanyin/project/prp43/deposit/ils/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00799, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_body_high.mrc Opened multi_ctf_c34_job27_body_high.mrc as #3, grid size 480,480,480, pixel 0.932, shown at level 0.0045, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_bottom_high.mrc Opened multi_ctf_c34_job27_bottom_high.mrc as #4, grid size 480,480,480, pixel 0.932, shown at level 0.000984, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_ntr_high.mrc Opened multi_ctf_c34_job27_ntr_high.mrc as #5, grid size 480,480,480, pixel 0.932, shown at level 0.000544, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/ils/multi/multi_ctf_c34_job27_prp43_high.mrc Opened multi_ctf_c34_job27_prp43_high.mrc as #6, grid size 480,480,480, pixel 0.932, shown at level 0.00086, step 2, values float32 > volume #3 step 1 level 0.01 > volume #4 step 1 level 0.01 > volume #5 step 1 level 0.01 > volume #6 step 1 level 0.01 > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM deep pink > color #1/6 /CB blue > color #1/A hot pink > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 dark khaki > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/Ci dark blue > color zone #2-10 near #1 distance 6 > view matrix camera > 0.50258,-0.032433,0.86392,748.17,-0.84845,0.17337,0.50008,539.22,-0.166,-0.98432,0.059613,259.91 > color #1/0 green yellow > color zone #2-10 near #1 distance 6 > hide #!1 models > save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view1.jpg > view matrix camera > 0.50258,-0.032433,0.86392,748.17,-0.84845,0.17337,0.50008,539.22,-0.166,-0.98432,0.059613,259.91 > save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view1.jpg > view matrix camera > 0.83999,0.11234,-0.53085,-119.57,0.50587,0.19174,0.84103,757.51,0.19627,-0.97499,0.10422,288.88 > save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view2.jpg > hide #1 target a > show #1 target r > hide #1/CM target r > show #1/2-8 target a > nucleotides #1/2-8 ladder > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > show #!1 models > hide #!1 models > graphics silhouettes true > view matrix camera > 0.50258,-0.032433,0.86392,748.17,-0.84845,0.17337,0.50008,539.22,-0.166,-0.98432,0.059613,259.91 > save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view1.jpg > view matrix camera > 0.83999,0.11234,-0.53085,-119.57,0.50587,0.19174,0.84103,757.51,0.19627,-0.97499,0.10422,288.88 > save /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_view2.jpg > show #!1 models > hide #1.2 models > view matrix camera > 0.50258,-0.032433,0.86392,748.17,-0.84845,0.17337,0.50008,539.22,-0.166,-0.98432,0.059613,259.91 > save > /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_model_view1.jpg > view matrix camera > 0.83999,0.11234,-0.53085,-119.57,0.50587,0.19174,0.84103,757.51,0.19627,-0.97499,0.10422,288.88 > save > /Users/lijuanyin/project/prp43/figure_new/figure1/ils_full_model_view2.jpg > close > open /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-41.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q1/c34_job28_Q1-coot-41.pdb --- warnings | Duplicate atom serial number found: 4205 Duplicate atom serial number found: 4206 Duplicate atom serial number found: 4207 Duplicate atom serial number found: 4208 Duplicate atom serial number found: 4209 1144 messages similar to the above omitted Chain information for c34_job28_Q1-coot-41.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CV | No description available CY | No description available Cb | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available P | No description available R | No description available S | No description available T | No description available V | No description available W | No description available Y | No description available Z | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available z | No description available > open /Users/lijuanyin/project/prp43/deposit/q1/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00702, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q1/local_ctf_c34_job28_2/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #3, grid size 480,480,480, pixel 0.932, shown at level 0.00705, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_body_2/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #4, grid size 480,480,480, pixel 0.932, shown at level 0.00635, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_dhx_2/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #5, grid size 480,480,480, pixel 0.932, shown at level 0.00258, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q1/multi/local_multi_ctf_c34_job28_head_2/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #6, grid size 480,480,480, pixel 0.932, shown at level 0.00276, step 2, values float32 > volume #2-10 step 1 level 0.005 > volume #4 step 1 level 0.0075 > volume #5 step 1 level 0.0065 > volume #6 step 1 level 0.005 > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc /R pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 green yellow > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/C deep pink > color #1/V steel blue > color #1/CV yellow green > color #1/8 red > color zone #2-10 near #1 distance 6 > view matrix camera > 0.52209,0.083337,-0.84881,-258.37,0.81484,0.24518,0.52528,513.08,0.25189,-0.96589,0.060097,268.61 > hide #!1 models > show #!1 models > color #1/CV magenta > color zone #2-10 near #1 distance 6 > hide #!1 models > view matrix camera > 0.52209,0.083337,-0.84881,-258.37,0.81484,0.24518,0.52528,513.08,0.25189,-0.96589,0.060097,268.61 > save /Users/lijuanyin/project/prp43/figure_new/figure2/q1_full_view1.jpg > view matrix camera > 0.10901,-0.19598,0.97453,779.23,-0.90425,0.38763,0.1791,312.85,-0.41285,-0.90074,-0.13496,161.59 > save /Users/lijuanyin/project/prp43/figure_new/figure2/q1_full_view2.jpg > hide #1 target a > show #1 target r > hide #1/CM target r > show #1/2-8 target a > nucleotides #1/2-8 ladder > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > show #!1 models > view matrix camera > 0.52209,0.083337,-0.84881,-258.37,0.81484,0.24518,0.52528,513.08,0.25189,-0.96589,0.060097,268.61 > save > /Users/lijuanyin/project/prp43/figure_new/figure2/q1_full_model_view1.jpg > view matrix camera > 0.10901,-0.19598,0.97453,779.23,-0.90425,0.38763,0.1791,312.85,-0.41285,-0.90074,-0.13496,161.59 > save > /Users/lijuanyin/project/prp43/figure_new/figure2/q1_full_model_view2.jpg > close > open /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-45.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/q2/c6_job26_Q2-coot-45.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 95 messages similar to the above omitted Chain information for c6_job26_Q2-coot-45.pdb #1 --- Chain | Description 0 | No description available 1 | No description available 2 | No description available 5 | No description available 6 | No description available 8 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available P | No description available R | No description available S | No description available T | No description available V | No description available W | No description available Y | No description available Z | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available z | No description available > open /Users/lijuanyin/project/prp43/deposit/q2/run_class001.mrc Opened run_class001.mrc as #2, grid size 480,480,480, pixel 0.932, shown at level 0.00639, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q2/local_c6_job26_2/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #3, grid size 480,480,480, pixel 0.932, shown at level 0.00615, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q2/multi/local_multi_c6_job26_body/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #4, grid size 480,480,480, pixel 0.932, shown at level 0.0055, step 2, values float32 > open > /Users/lijuanyin/project/prp43/deposit/q2/multi/local_multi_c6_job26_head/relion_locres_filtered.mrc Opened relion_locres_filtered.mrc as #5, grid size 480,480,480, pixel 0.932, shown at level 0.00246, step 2, values float32 > volume #2-10 step 1 level 0.0045 > volume #4 step 1 level 0.0075 > volume #5 step 1 level 0.003 > volume #4 step 1 level 0.0055 > surface dust #1-15 size 20 > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U cyan > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 green yellow > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > color #1/R dark violet > color #1/F deep sky blue > color #1/2 lime > color #1/5 hot pink > color #1/Y olive > color #1/E tomato > color #1/C deep pink > color #1/V steel blue > color #1/CV magenta > color #1/8 red > color zone #2-10 near #1 distance 6 > view matrix camera > 0.52209,0.083337,-0.84881,-259.14,0.81484,0.24518,0.52528,513.87,0.25189,-0.96589,0.060097,250.86 > hide #!1 models > view matrix camera > 0.52209,0.083337,-0.84881,-259.14,0.81484,0.24518,0.52528,513.87,0.25189,-0.96589,0.060097,250.86 > save /Users/lijuanyin/project/prp43/figure_new/figure2/q2_full_view1.jpg > view matrix camera > 0.10901,-0.19598,0.97453,776.31,-0.90425,0.38763,0.1791,317.57,-0.41285,-0.90074,-0.13496,146.75 > save /Users/lijuanyin/project/prp43/figure_new/figure2/q2_full_view2.jpg > hide #1 target a > show #1 target r > hide #1/CM target r > show #1/2-8 target a > nucleotides #1/2-8 ladder > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > show #!1 models > view matrix camera > 0.52209,0.083337,-0.84881,-259.14,0.81484,0.24518,0.52528,513.87,0.25189,-0.96589,0.060097,250.86 > save > /Users/lijuanyin/project/prp43/figure_new/figure2/q2_full_model_view1.jpg > view matrix camera > 0.10901,-0.19598,0.97453,776.31,-0.90425,0.38763,0.1791,317.57,-0.41285,-0.90074,-0.13496,146.75 > save > /Users/lijuanyin/project/prp43/figure_new/figure2/q2_full_model_view2.jpg > close > open /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/ils/c34_job27_ILS-coot-41.pdb --- warnings | Duplicate atom serial number found: 1 Duplicate atom serial number found: 2 Duplicate atom serial number found: 3 Duplicate atom serial number found: 4 Duplicate atom serial number found: 5 95 messages similar to the above omitted Chain information for c34_job27_ILS-coot-41.pdb #1 --- Chain | Description 0 | No description available 2 | No description available 5 | No description available 6 | No description available 7 | No description available A | No description available B | No description available C | No description available CY | No description available Cb | No description available Cc | No description available Ci | No description available D | No description available E | No description available F | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available P | No description available R | No description available S | No description available T | No description available U | No description available W | No description available Y | No description available a | No description available b | No description available c | No description available d | No description available e | No description available f | No description available g | No description available h | No description available i | No description available j | No description available k | No description available l | No description available m | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available u | No description available > open /Users/lijuanyin/project/prp43/deposit/published/8ro1-ils_2.cif- > coot-0.cif Summary of feedback from opening /Users/lijuanyin/project/prp43/deposit/published/8ro1-ils_2.cif-coot-0.cif --- warnings | Skipping chem_comp category: Missing column 'type' on line 141 Missing entity information. Treating each chain as a separate entity. Missing or incomplete sequence information. Inferred polymer connectivity. Skipping chem_comp category: Missing column 'type' on line 120723 Skipping chem_comp category: Missing column 'type' on line 120750 Skipping chem_comp category: Missing column 'type' on line 120777 Skipping chem_comp category: Missing column 'type' on line 121056 Skipping chem_comp category: Missing column 'type' on line 121308 3 messages similar to the above omitted Chain information for 8ro1-ils_2.cif-coot-0.cif #2 --- Chain | Description 2 | No description available 5 | No description available 6 | No description available A | No description available C | No description available D | No description available DX | No description available E | No description available I | No description available IN | No description available J | No description available K | No description available L | No description available L1 | No description available L2 | No description available M | No description available N | No description available O | No description available P | No description available PX | No description available Q | No description available R | No description available S | No description available T | No description available TF | No description available W | No description available X | No description available Z | No description available a h | No description available b | No description available c j | No description available d | No description available e l | No description available f m | No description available g n | No description available i | No description available k | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available y | No description available > open /Users/lijuanyin/project/prp43/deposit/published/5y88-ILS.cif- > coot-0.pdb Chain information for 5y88-ILS.cif-coot-0.pdb #3 --- Chain | Description A | No description available B | No description available C | No description available D | No description available E | No description available F | No description available G | No description available H | No description available I | No description available J | No description available K | No description available L | No description available M | No description available N | No description available O | No description available P | No description available Q | No description available R | No description available S | No description available T | No description available U | No description available V | No description available W | No description available a | No description available b i | No description available c j | No description available d k | No description available e l | No description available f m | No description available g | No description available h | No description available n | No description available o | No description available p | No description available q | No description available r | No description available s | No description available t | No description available x | No description available > surface dust #1-15 size 20 No surfaces specified > set bgColor white > windowsize 800 800 > color #1 #3-10 silver > color #1 cyan > color #2-10 silver > color #1/a-g /j-p /u sienna > color #1/K /L /P /R /T /q-t /CW wheat > color #1/F /V /W /Z /CN sky blue > color #1/B /Ca plum > color #1/D /G /H /Q /X green > color #1/I /Y /CV light green > color #1/J /M /N /S /CY /Cb /Cc pink > color #1/CD /CK /CL orange > color #1/CR /CT /CX /CZ lime > color #1/O /CA /CC /CU purple > color #1/2 /h /i /CS cornflower blue > color #1/CP /CQ /CE /CF /CG /CI /CJ forest green > color #1/5 /A /C /E /CM hot pink > color #1/6 /CB blue > color #1/7 red > color #1/8 magenta > color #1/M dark red > color #1/Cc orange > color #1/U lime > color #1/Cb dodger blue > color #1/CY dark red > color #1/0 green yellow > color #1/Ch aquamarine > color #1/Cf cyan > color #1/Cd teal > color #1/z tomato > color #1/1 forest green > color #1/Cg chocolate > hide #1-2 target a > show #1-2 target r > hide #1/CM target r > show #1-2/2-8 target a > nucleotides #1-2/2-8 #2/N ladder > color #1-2 silver > color #2/L1 purple > color #1/Cb #2/TF dodger blue > color #1/CY #2/PX dark red > color #1/M dark red > color #1/0 #2/O green yellow > color #1/Cc #2/DX orange > color #1/B #2/M plum > color #1/D #2/X green > color #1-2/6 blue > color #1-2/I light green > ribbon style protein modeh tube rad 2 sides 24 > ribbon style nucleic xsect rect width 3.2 thick 1.6 > cartoon style protein xsection oval width 3.2 thickness 1 > cartoon style strand xsection rectangle width 3.2 thickness 1.6 > hide #!1 models > hide #!2 models > show #!3 cartoons > hide #!3 atoms > show #!1 models > color #1-2 silver > color #1/M #3/M dark red > color #1/0 #2/O #3/N green yellow > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > hide #!1 models > show #!2 models > hide #!3 models > hide #!2 models > show #!1 models > hide #1.2 models > hide #2.1 models > hide #3.1 models > show #!2 models > show #!3 models > ui tool show ""Side View"" > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > hide #!2 models > view matrix view matrix camera -0.7213,0.50409,0.47499,348.06,-0.51049,0.076562,-0.85647,37.098,-0.4681,-0.86025,0.20211,231.59 view matrix models #1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,1,0,0,0,0,1,0,0,0,0,1,0,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#3,1,0,0,0,0,1,0,0,0,0,1,0,#3.1,1,0,0,0,0,1,0,0,0,0,1,0 > show #!1 models > hide #!3 models > save > /Users/lijuanyin/project/prp43/figure_new/figure_s2/ils_ecm2_model_view3.jpg > show #!2 models > hide #!1 models > save > /Users/lijuanyin/project/prp43/figure_new/figure_s2/8ro1_ecm2_model_view3.jpg > show #!3 models > hide #!2 models > save > /Users/lijuanyin/project/prp43/figure_new/figure_s2/5y88_ecm2_model_view3.jpg ===== Log before crash end ===== Log: Startup Messages --- warning | QCoreApplication::postEvent: Unexpected null receiver note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9rc202410310525 (2024-10-31) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 ATI-6.1.13 OpenGL renderer: AMD Radeon Pro 5500M OpenGL Engine OpenGL vendor: ATI Technologies Inc. Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,1 Processor Name: 8-Core Intel Core i9 Processor Speed: 2,3 GHz Number of Processors: 1 Total Number of Cores: 8 L2 Cache (per Core): 256 KB L3 Cache: 16 MB Hyper-Threading Technology: Enabled Memory: 64 GB System Firmware Version: 2069.0.0.0.0 (iBridge: 22.16.10353.0.0,0) OS Loader Version: 582~1023 Software: System Software Overview: System Version: macOS 15.0 (24A335) Kernel Version: Darwin 24.0.0 Time since boot: 32天2小时30分钟 Graphics/Displays: Intel UHD Graphics 630: Chipset Model: Intel UHD Graphics 630 Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x3e9b Revision ID: 0x0002 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 AMD Radeon Pro 5500M: Chipset Model: AMD Radeon Pro 5500M Type: GPU Bus: PCIe PCIe Lane Width: x16 VRAM (Total): 8 GB Vendor: AMD (0x1002) Device ID: 0x7340 Revision ID: 0x0040 ROM Revision: 113-D3220E-190 VBIOS Version: 113-D32206U1-020 Option ROM Version: 113-D32206U1-020 EFI Driver Version: 01.A1.190 Automatic Graphics Switching: Supported gMux Version: 5.0.0 Metal Support: Metal 3 Displays: C34H89x: Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD) UI Looks like: 3440 x 1440 @ 50.00Hz Framebuffer Depth: 30-Bit Color (ARGB2101010) Display Serial Number: H1AK500000 Main Display: Yes Mirror: Off Online: Yes Rotation: Supported Adapter Type: Apple USB-C Digital AV Adapter Adapter Firmware Version: 2,35 Installed Packages: alabaster: 1.0.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 2.4.1 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 2.7.1 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.17 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.7 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.4.7 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9rc202410310525 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.5 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: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2 ChimeraX-Label: 1.1.11 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 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: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.1 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.17 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-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: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 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: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.2.3 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 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: 1.18.1 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 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: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.0 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.7 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.54.1 funcparserlib: 2.0.0a0 glfw: 2.7.0 grako: 3.16.5 h5py: 3.12.1 html2text: 2024.2.26 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.1 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.1 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 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 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.1 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX