id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15842 Graphics crash, macOS 14.6.1, Intel Iris Plus Graphics chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Aborted Current thread 0x00007ff854e1ddc0 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2772 in draw_elements File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1749 in draw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 852 in _draw_geometry File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 787 in draw_self File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 780 in draw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1567 in _draw_multiple File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1554 in draw_opaque File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 258 in _draw_scene File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 288 in render File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 113 in _redraw File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 149 in invoke File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 248 in _activate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 217 in activate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/triggerset.py"", line 393 in activate_trigger File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 100 in draw_new_frame File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.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-1.7.1.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: 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""experimentId"" : ""6643969b3099cf28e049862f"", ""deploymentId"" : 400000007 } ] } } ===== Log before crash start ===== Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/butryna/Desktop/Fig5/Fig5_ATPase.cxs Opened vopmax_A_EMR.mrc as #5, grid size 440,440,440, pixel 0.95, shown at level 0.21, step 2, values float32 Opened Unoccupied.mrc 0 as #1.1, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Orc1.mrc 1 as #1.2, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Orc6.mrc 2 as #1.3, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Lagging.mrc 3 as #1.4, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Leading.mrc 4 as #1.5, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Orc2.mrc 5 as #1.6, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Mcm4.mrc 6 as #1.7, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Mcm5.mrc 7 as #1.8, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Orc4.mrc 8 as #1.9, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Orc3.mrc 9 as #1.10, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened vopmax_A_EMR.mrc 10 as #1.11, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Cdt1.mrc 11 as #1.12, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Mcm7.mrc 12 as #1.13, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Mcm2.mrc 13 as #1.14, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Mcm3.mrc 14 as #1.15, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 Opened Orc5.mrc 15 as #1.16, grid size 440,440,440, pixel 0.95, shown at level 2.04, step 1, values float32 opened ChimeraX session > open > /Users/butryna/Documents/Phenix/krios_5RA/RealSpaceRefine_123/OCCM_vopmaxA_isolde_noH- > coot-17_OXT_real_space_refined_123.pdb Chain information for OCCM_vopmaxA_isolde_noH- coot-17_OXT_real_space_refined_123.pdb #2 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | 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 X Y | No description available > show cartoons > hide atoms > hide #!3 models > dssp > ui tool show ""Side View"" > select #2/y 861 atoms, 965 bonds, 42 residues, 1 model selected > color sel red > select #2/x 861 atoms, 965 bonds, 42 residues, 1 model selected > ui tool show ""Color Actions"" > select #2/x 861 atoms, 965 bonds, 42 residues, 1 model selected > select clear > select #2/x 861 atoms, 965 bonds, 42 residues, 1 model selected > color sel #ffffffff > color sel white > select clear > select #2/2 5087 atoms, 5174 bonds, 6 pseudobonds, 639 residues, 3 models selected > color (#!2 & sel) #00ff77ff > color (#!2 & sel) #b7ff9dff > select #2/6 5436 atoms, 5524 bonds, 12 pseudobonds, 679 residues, 3 models selected > color (#!2 & sel) #246b05ff > select #2/7 4542 atoms, 4609 bonds, 11 pseudobonds, 578 residues, 3 models selected > color (#!2 & sel) #6b8e23ff > select #2/3 4583 atoms, 4661 bonds, 4 pseudobonds, 585 residues, 2 models selected > color (#!2 & sel) #7fff00ff > select #2/5 5087 atoms, 5160 bonds, 11 pseudobonds, 640 residues, 3 models selected > color (#!2 & sel) #228b22ff > select clear > select #2/8 4047 atoms, 4123 bonds, 3 pseudobonds, 505 residues, 2 models selected > color (#!2 & sel) #d3d3d3ff > select #2/a 961 atoms, 971 bonds, 120 residues, 1 model selected > color sel #8b4513ff > select #2/f 324 atoms, 328 bonds, 38 residues, 1 model selected > color sel #e1bae0ff > select #2/b 1845 atoms, 1892 bonds, 3 pseudobonds, 222 residues, 2 models selected > color (#!2 & sel) #ff7f50ff > select #2/d 3573 atoms, 3639 bonds, 3 pseudobonds, 435 residues, 2 models selected > color (#!2 & sel) #ffa500ff > select #2/c 4618 atoms, 4717 bonds, 3 pseudobonds, 557 residues, 2 models selected > color (#!2 & sel) #e9967aff > select #2/e 3475 atoms, 3559 bonds, 3 pseudobonds, 421 residues, 2 models selected > color (#!2 & sel) #8b0000ff > select #2/4 4992 atoms, 5053 bonds, 13 pseudobonds, 628 residues, 3 models selected > color (#!2 & sel) #b7ff9dff > select clear > select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f 33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected > cartoon hide (#!2 & sel) > select #2/x/y 1722 atoms, 1930 bonds, 84 residues, 1 model selected > cartoon sel > select clear > select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385 12703 atoms, 12934 bonds, 16 pseudobonds, 1586 residues, 2 models selected > select up 12783 atoms, 13012 bonds, 16 pseudobonds, 1596 residues, 2 models selected > select up 20297 atoms, 20624 bonds, 16 pseudobonds, 2582 residues, 2 models selected > select #2/c/6:902-1500/4:730-1500/5:706-1500 7194 atoms, 7324 bonds, 8 pseudobonds, 867 residues, 2 models selected > select #2/c/6:902-1500/4:854-1500/5:706-1500 6407 atoms, 6529 bonds, 5 pseudobonds, 768 residues, 2 models selected > cartoon hide (#!2 & sel) > save Fig4.cxs format session > select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f 33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected > select #2/2473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 14121 atoms, 14297 bonds, 16 pseudobonds, 1799 residues, 2 models selected > surface (#!2 & sel) > transparency (#!2 & sel) 70 > select #2 50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 3 models selected > cartoon hide (#!2 & sel) > select > #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x 3185 atoms, 3389 bonds, 2 pseudobonds, 284 residues, 2 models selected > cartoon (#!2 & sel) > select clear > lighting simple > select #2/2473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 14121 atoms, 14297 bonds, 16 pseudobonds, 1799 residues, 2 models selected > select #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected > surface (#!2 & sel) > transparency (#!2 & sel) 70 > select clear > select #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected > select > #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x 3185 atoms, 3389 bonds, 2 pseudobonds, 284 residues, 2 models selected > select #2 50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 3 models selected > surface hidePatches (#!2 & sel) > select > #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x 3185 atoms, 3389 bonds, 2 pseudobonds, 284 residues, 2 models selected > select ~sel & ##selected 47107 atoms, 47951 bonds, 70 pseudobonds, 5847 residues, 3 models selected > surface (#!2 & sel) > select up 47130 atoms, 47951 bonds, 70 pseudobonds, 5870 residues, 16 models selected > select up 47271 atoms, 48092 bonds, 70 pseudobonds, 5870 residues, 16 models selected > select up 47456 atoms, 48276 bonds, 70 pseudobonds, 5899 residues, 16 models selected > select up 48570 atoms, 49410 bonds, 70 pseudobonds, 6047 residues, 16 models selected > select up 50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 16 models selected > select up 50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 16 models selected > select up 50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 16 models selected > select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f 33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected > surface (#!2 & sel) > surface hidePatches (#!2 & sel) > select #2 50292 atoms, 51340 bonds, 72 pseudobonds, 6131 residues, 3 models selected > surface (#!2 & sel) > select #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f 33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected > surface hidePatches (#!2 & sel) > select up 33348 atoms, 34171 bonds, 31 pseudobonds, 3978 residues, 17 models selected > select up 40862 atoms, 41783 bonds, 31 pseudobonds, 4964 residues, 17 models selected > select up 41021 atoms, 41939 bonds, 31 pseudobonds, 4986 residues, 17 models selected > select up 45238 atoms, 46217 bonds, 31 pseudobonds, 5515 residues, 17 models selected > select up 45336 atoms, 46312 bonds, 31 pseudobonds, 5527 residues, 17 models selected > select up 48585 atoms, 49618 bonds, 31 pseudobonds, 5927 residues, 17 models selected > select up 48632 atoms, 49663 bonds, 31 pseudobonds, 5934 residues, 17 models selected > select up 49678 atoms, 50722 bonds, 31 pseudobonds, 6061 residues, 17 models selected > select up 49709 atoms, 50751 bonds, 31 pseudobonds, 6065 residues, 17 models selected > select up 50071 atoms, 51117 bonds, 31 pseudobonds, 6109 residues, 17 models selected > select > #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467 1463 atoms, 1459 bonds, 2 pseudobonds, 200 residues, 2 models selected > surface hidePatches (#!2 & sel) > select clear > select > #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467 1463 atoms, 1459 bonds, 2 pseudobonds, 200 residues, 2 models selected > surface (#!2 & sel) > select #2/2473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 14121 atoms, 14297 bonds, 16 pseudobonds, 1799 residues, 2 models selected > surface (#!2 & sel) > select clear > select #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected > surface (#!2 & sel) > select clear > select #2/7/3 9125 atoms, 9270 bonds, 15 pseudobonds, 1163 residues, 3 models selected > cartoon hide (#!2 & sel) > surface hidePatches (#!2 & sel) > select #2/c/6:902-1500/4:854-1500/5:706-1500 6407 atoms, 6529 bonds, 5 pseudobonds, 768 residues, 2 models selected > surface hidePatches (#!2 & sel) > select #2/7/3 9125 atoms, 9270 bonds, 15 pseudobonds, 1163 residues, 3 models selected > surface (#!2 & sel) > select clear > select #2/7/3 9125 atoms, 9270 bonds, 15 pseudobonds, 1163 residues, 3 models selected > surface hidePatches (#!2 & sel) > select #2/3:339-1500/7:386-1500 4844 atoms, 4902 bonds, 4 pseudobonds, 624 residues, 2 models selected > surface (#!2 & sel) > transparency (#!2 & sel) 0 > select clear > close #1 > close #3,5 > open > /Users/butryna/Documents/Phenix/2RA/RealSpaceRefine_38/ref11_ref13_DNAFFed- > coot-12_isolde_noH_Zn_OXT_real_space_refined_038.pdb Chain information for ref11_ref13_DNAFFed- coot-12_isolde_noH_Zn_OXT_real_space_refined_038.pdb #1 --- Chain | Description 2 | No description available 3 | No description available 4 | No description available 5 | No description available 6 | No description available 7 | No description available 8 | 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 X Y | No description available > hide atoms > hide cartoons > show cartoons > mmaker #1/6 to #2/6 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker OCCM_vopmaxA_isolde_noH-coot-17_OXT_real_space_refined_123.pdb, chain 6 (#2) with ref11_ref13_DNAFFed- coot-12_isolde_noH_Zn_OXT_real_space_refined_038.pdb, chain 6 (#1), sequence alignment score = 3301.1 RMSD between 640 pruned atom pairs is 0.993 angstroms; (across all 672 pairs: 1.114) > dssp > select #1/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f 35198 atoms, 36055 bonds, 36 pseudobonds, 4204 residues, 2 models selected > hide sel cartoons > select > #1/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f/8 35198 atoms, 36055 bonds, 36 pseudobonds, 4204 residues, 2 models selected > hide sel cartoons > hide #!2 models > show #!2 models > hide #!1 models > select > #2/2:1-472/3:1-338/4:1-498/5:1-344/6:1-508/7:1-385/x/y/8/a/b/c/d/e/f/8 33268 atoms, 34093 bonds, 31 pseudobonds, 3968 residues, 2 models selected > hide sel cartoons > select #2/c/6:902-1500/4:854-1500/5:706-1500 6407 atoms, 6529 bonds, 5 pseudobonds, 768 residues, 2 models selected > hide sel cartoons > select #1/c/6:902-1500/4:854-1500/5:706-1500 5948 atoms, 6059 bonds, 5 pseudobonds, 716 residues, 2 models selected > hide #!2 cartoons > select #1/c/6:902-1500/4:854-1500/5:706-1500 5948 atoms, 6059 bonds, 5 pseudobonds, 716 residues, 2 models selected > select #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected > show sel cartoons > hide sel cartoons > select > #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x 3185 atoms, 3389 bonds, 2 pseudobonds, 284 residues, 2 models selected > show sel cartoons > show #!1 models > hide #!2 models > select #1/6:902-1500/4:854-1500/5:706-1500 1367 atoms, 1380 bonds, 1 pseudobond, 164 residues, 2 models selected > select #1/6:902-1500/4:854-1500/5:706-1500/7:740-1500 1819 atoms, 1838 bonds, 1 pseudobond, 218 residues, 2 models selected > hide sel cartoons > select #1/2 4709 atoms, 4787 bonds, 3 pseudobonds, 592 residues, 2 models selected > ui tool show ""Color Actions"" > color (#!1 & sel) #00ff77ff > select #1/4 5253 atoms, 5318 bonds, 11 pseudobonds, 660 residues, 3 models selected > color (#!1 & sel) #b7ff9dff > select #1/6 5448 atoms, 5538 bonds, 11 pseudobonds, 681 residues, 3 models selected > color (#!1 & sel) #246b05ff > select #1/7 5156 atoms, 5233 bonds, 10 pseudobonds, 653 residues, 3 models selected > color (#!1 & sel) #6b8e23ff > select #1/3 4516 atoms, 4594 bonds, 6 pseudobonds, 574 residues, 2 models selected > color (#!1 & sel) #7fff00ff > select #1/5 4488 atoms, 4550 bonds, 10 pseudobonds, 568 residues, 3 models selected > color (#!1 & sel) #228b22ff > select #1/y 861 atoms, 965 bonds, 42 residues, 1 model selected > color sel #ff0000ff > select #1/x 861 atoms, 965 bonds, 42 residues, 1 model selected > color sel #ffffffff > select #1/x/y 1722 atoms, 1930 bonds, 84 residues, 1 model selected > show sel cartoons > show #!2 models > hide #!2 models > select > #1/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/y/x 3282 atoms, 3488 bonds, 1 pseudobond, 298 residues, 2 models selected > select up 3430 atoms, 3635 bonds, 1 pseudobond, 323 residues, 2 models selected > select up 13067 atoms, 13426 bonds, 1 pseudobond, 1562 residues, 2 models selected > select > #1/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/y/x 18884 atoms, 19314 bonds, 14 pseudobonds, 2269 residues, 2 models selected > hide sel cartoons > show sel cartoons > select ~sel & ##selected 33497 atoms, 34150 bonds, 56 pseudobonds, 4120 residues, 3 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > select #1 18884 atoms, 19314 bonds, 14 pseudobonds, 2269 residues, 2 models selected > show sel cartoons > select #1/6:902-1500/4:854-1500/5:706-1500/7:740-1500 1819 atoms, 1838 bonds, 1 pseudobond, 218 residues, 2 models selected > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > show #!2 models > hide #!1 models > select > #1/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/y/x 17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 2 models selected > select > #2/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/y/x 18724 atoms, 19152 bonds, 17 pseudobonds, 2246 residues, 2 models selected > select ~sel & ##selected 31568 atoms, 32188 bonds, 55 pseudobonds, 3885 residues, 3 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > save Fig4.cxs format session > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > ui tool show ""Selection Inspector"" > setattr =sel p display false Assigning display attribute to 1 item > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > select #2/5/2/4/6 12158 atoms, 12320 bonds, 13 pseudobonds, 1538 residues, 2 models selected > transparency (#!2 & sel) 70 > select clear > select #2/3/7 4844 atoms, 4902 bonds, 4 pseudobonds, 624 residues, 2 models selected > surface hidePatches (#!2 & sel) > hide sel cartoons > show #!1 models > hide #!2 models > select #2/3 2409 atoms, 2437 bonds, 2 pseudobonds, 309 residues, 2 models selected > hide #!1 cartoons > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > select #1 17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 2 models selected > show sel cartoons > select #1/3 2370 atoms, 2399 bonds, 3 pseudobonds, 302 residues, 2 models selected > hide sel cartoons > select #1/3 2370 atoms, 2399 bonds, 3 pseudobonds, 302 residues, 2 models selected > show sel cartoons > select #1/3 2370 atoms, 2399 bonds, 3 pseudobonds, 302 residues, 2 models selected > hide sel cartoons > select #1/5/7 5162 atoms, 5227 bonds, 2 pseudobonds, 666 residues, 2 models selected > surface (#!1 & sel) > show #!2 models > hide #!1 models > show #!1 models > hide #!2 models > select #1 17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 3 models selected > surface (#!1 & sel) > select #1/x/y 1722 atoms, 1930 bonds, 84 residues, 1 model selected > surface hidePatches (#!1 & sel) > select #1/2/4/6/5 10376 atoms, 10516 bonds, 7 pseudobonds, 1329 residues, 2 models selected > transparency (#!1 & sel) 70 > select #1/3 2370 atoms, 2399 bonds, 3 pseudobonds, 302 residues, 2 models selected > surface hidePatches (#!1 & sel) > select #1 17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 5 models selected > surface hidePatches (#!1 & sel) > select clear > select #1 17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 5 models selected > select #1/2/3/4/5/6/7 15343 atoms, 15546 bonds, 10 pseudobonds, 1967 residues, 2 models selected > surface (#!1 & sel) > transparency (#!1 & sel) 70 > select #2/2/3/4/5/6/7 17002 atoms, 17222 bonds, 17 pseudobonds, 2162 residues, 2 models selected > surface #1 > transparency #1 70 > hide #!1 models > show #!2 models > select #2 18724 atoms, 19152 bonds, 17 pseudobonds, 2246 residues, 2 models selected > surface (#!2 & sel) > select #2/x/y 1722 atoms, 1930 bonds, 84 residues, 1 model selected > surface hidePatches (#!2 & sel) > select #2 18724 atoms, 19152 bonds, 17 pseudobonds, 2246 residues, 2 models selected > transparency (#!2 & sel) 70 > show #!1 models > hide #!2 models > select #1/x/y 1722 atoms, 1930 bonds, 84 residues, 1 model selected > surface hidePatches (#!1 & sel) > select #1/2/3/4/5/6/7 15343 atoms, 15546 bonds, 10 pseudobonds, 1967 residues, 2 models selected > hide sel cartoons > hide #!1 models > show #!2 models > show #!2 cartoons > hide #!2 cartoons > show #!2 cartoons > hide #!2 cartoons > select #2/x/y 1722 atoms, 1930 bonds, 84 residues, 1 model selected > show sel cartoons > show #!1 models > hide #!2 models > select > #2/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467 1463 atoms, 1459 bonds, 2 pseudobonds, 200 residues, 2 models selected > hide #!1 models > show #!2 models > show sel cartoons > show #!1 models > hide #!2 models > select > #1/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467 1560 atoms, 1558 bonds, 1 pseudobond, 214 residues, 2 models selected > show sel cartoons > select clear > save Fig4.cxs format session Enter a PDB ID in the entry field > open 5v8f fromDatabase pdb format mmcif Summary of feedback from opening 5v8f fetched from pdb --- warning | Atom CE has no neighbors to form bonds with according to residue template for MET /6:313 5v8f title: Structural basis of MCM2-7 replicative helicase loading by ORC-Cdc6 and Cdt1 [more info...] Chain information for 5v8f #3 --- Chain | Description | UniProt 2 | DNA replication licensing factor MCM2 | MCM2_YEAST 1-868 3 | DNA replication licensing factor MCM3 | MCM3_YEAST 1-961 4 | DNA replication licensing factor MCM4 | MCM4_YEAST 1-933 5 | Minichromosome maintenance protein 5 | MCM5_YEAST 1-775 6 | DNA replication licensing factor MCM6 | MCM6_YEAST 1-1017 7 | DNA replication licensing factor MCM7 | MCM7_YEAST 1-800 8 | Cell division cycle protein CDT1 | CDT1_YEAST 1-604 9 | Cell division control protein 6 | CDC6_YEAST 1-513 A | Origin recognition complex subunit 1 | ORC1_YEAST 1-913 B | Origin recognition complex subunit 2 | ORC2_YEAST 1-620 C | Origin recognition complex subunit 3 | ORC3_YEAST 1-616 D | Origin recognition complex subunit 4 | ORC4_YEAST 1-529 E | Origin recognition complex subunit 5 | ORC5_YEAST 1-479 F | Origin recognition complex subunit 6 | ORC6_YEAST 1-435 M | DNA (39-MER) | N | DNA (39-MER) | Non-standard residues in 5v8f #3 --- AGS — phosphothiophosphoric acid-adenylate ester (atp-γ-S; adenosine 5'-(3-thiotriphosphate); adenosine 5'-(γ-thiotriphosphate); adenosine-5'-diphosphate monothiophosphate) > hide #!1,3 atoms > hide #!1 models > select #3/2473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 15194 atoms, 15386 bonds, 7 pseudobonds, 1941 residues, 2 models selected > show sel cartoons > select #3/2/473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500 19960 atoms, 20228 bonds, 10 pseudobonds, 2545 residues, 2 models selected > select > #3/2/473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/m/n 21559 atoms, 22020 bonds, 83 pseudobonds, 2623 residues, 3 models selected > show sel cartoons > select ~sel & ##selected 38027 atoms, 38739 bonds, 39 pseudobonds, 4682 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select #1/6:902-1500/4:854-1500/5:706-1500/7:740-1500 Nothing selected > select #3/6:902-1500/4:854-1500/5:706-1500/7:740-1500 1705 atoms, 1722 bonds, 205 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3/3:892-1500 565 atoms, 573 bonds, 69 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3/7:731 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 133 atoms, 133 bonds, 16 residues, 1 model selected > select down 7 atoms, 6 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select clear > select #3/7:732 8 atoms, 7 bonds, 1 residue, 1 model selected > select up 126 atoms, 125 bonds, 15 residues, 1 model selected > select down 8 atoms, 7 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select #3/7:733 9 atoms, 8 bonds, 1 residue, 1 model selected > select up 118 atoms, 117 bonds, 14 residues, 1 model selected > select down 9 atoms, 8 bonds, 1 residue, 1 model selected > delete atoms sel > delete bonds sel > select #3/7:734 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 109 atoms, 108 bonds, 13 residues, 1 model selected > select down 6 atoms, 5 bonds, 1 residue, 1 model selected > select clear > select #3/7:734-739 47 atoms, 46 bonds, 6 residues, 1 model selected > delete atoms sel > delete bonds sel > select > #3/2:473-1500/3:339-1500/4:499-1500/5:335-1500/6:509-1500/7:386-1500/m/n 17306 atoms, 17707 bonds, 78 pseudobonds, 2097 residues, 3 models selected > select ~sel & ##selected 1912 atoms, 1946 bonds, 2 pseudobonds, 243 residues, 2 models selected > delete atoms (#!3 & sel) > delete bonds (#!3 & sel) > select #3/5:335 6 atoms, 5 bonds, 1 residue, 1 model selected > select up 74 atoms, 72 bonds, 10 residues, 1 model selected > delete atoms sel > delete bonds sel > select #3/2 2854 atoms, 2896 bonds, 1 pseudobond, 361 residues, 2 models selected > ui tool show ""Color Actions"" > color (#!3 & sel) #00ff77ff > select #3/4 2718 atoms, 2755 bonds, 348 residues, 1 model selected > color sel #b7ff9dff > select #3/6 2536 atoms, 2573 bonds, 326 residues, 1 model selected > color sel #246b05ff > select #3/7 2623 atoms, 2657 bonds, 1 pseudobond, 339 residues, 2 models selected > color (#!3 & sel) #6b8e23ff > select #3/3 2474 atoms, 2503 bonds, 1 pseudobond, 320 residues, 2 models selected > color (#!3 & sel) #7fff00ff > select #3/5 2428 atoms, 2458 bonds, 1 pseudobond, 315 residues, 2 models selected > color (#!3 & sel) #228b22ff > select #3/y Nothing selected > color #3 #ffffffff > color #3 #ff0000ff > select #3/x Nothing selected > color #3 #ffffffff > select #3/x Nothing selected > select #3/2 2854 atoms, 2896 bonds, 1 pseudobond, 361 residues, 2 models selected > color (#!3 & sel) #00ff77ff > select #3/4 2718 atoms, 2755 bonds, 348 residues, 1 model selected > color sel #b7ff9dff > select #3/6 2536 atoms, 2573 bonds, 326 residues, 1 model selected > color sel #246b05ff > select #3/7 2623 atoms, 2657 bonds, 1 pseudobond, 339 residues, 2 models selected > color (#!3 & sel) #6b8e23ff > select #3/3 2474 atoms, 2503 bonds, 1 pseudobond, 320 residues, 2 models selected > color (#!3 & sel) #7fff00ff > select #3/5 2428 atoms, 2458 bonds, 1 pseudobond, 315 residues, 2 models selected > color (#!3 & sel) #228b22ff > select #3/m 795 atoms, 886 bonds, 39 residues, 1 model selected > color sel #ff0000ff > select #3/n 804 atoms, 906 bonds, 39 residues, 1 model selected > color sel #ffffffff > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > mmaker #3/6 to #1/6 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker ref11_ref13_DNAFFed- coot-12_isolde_noH_Zn_OXT_real_space_refined_038.pdb, chain 6 (#1) with 5v8f, chain 6 (#3), sequence alignment score = 2422.7 RMSD between 305 pruned atom pairs is 0.851 angstroms; (across all 319 pairs: 1.052) > show #!2 models > show #!1 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!3 models > hide #!3 models > show #!2 models > select #2 18724 atoms, 19152 bonds, 17 pseudobonds, 2246 residues, 2 models selected > surface hidePatches (#!2 & sel) > select #2/6:902-1500/4:854-1500/5:706-1500/7:740-1500 1790 atoms, 1812 bonds, 2 pseudobonds, 212 residues, 2 models selected > delete atoms (#!2 & sel) > delete bonds (#!2 & sel) > select #2/2/3/4/5/6/7 15212 atoms, 15410 bonds, 12 pseudobonds, 1950 residues, 2 models selected > surface (#!2 & sel) > select clear > show #!1 models > hide #!2 models > show #!2 models > show #!3 models > hide #!1 models > hide #!2 models > select #3 17232 atoms, 17634 bonds, 77 pseudobonds, 2087 residues, 3 models selected > surface (#!3 & sel) > transparency (#!3 & sel) 70 > select #3/m/n 1599 atoms, 1792 bonds, 73 pseudobonds, 78 residues, 2 models selected > surface hidePatches (#!3 & sel) > select > #3/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467/m/n 3207 atoms, 3399 bonds, 73 pseudobonds, 300 residues, 2 models selected > select ~sel & ##selected 14025 atoms, 14235 bonds, 4 pseudobonds, 1787 residues, 2 models selected > cartoon hide (#!3 & sel) > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > hide #!3 models > show #!3 models > hide #!2 models > select #3/m 795 atoms, 886 bonds, 39 residues, 1 model selected > color (#!3 & sel) white > select #3/n 804 atoms, 906 bonds, 39 residues, 1 model selected > color (#!3 & sel) red > select clear > show #!2 models > hide #!2 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > hide #!1 models > select #3/3 2474 atoms, 2503 bonds, 1 pseudobond, 320 residues, 2 models selected > hide sel cartoons > surface hidePatches (#!3 & sel) > select #3/7 2623 atoms, 2657 bonds, 1 pseudobond, 339 residues, 2 models selected > surface hidePatches (#!3 & sel) > hide sel cartoons > select #3/4 2718 atoms, 2755 bonds, 348 residues, 1 model selected > surface hidePatches (#!3 & sel) > cartoon hide (#!3 & sel) > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting simple > lighting full > select #3 17232 atoms, 17634 bonds, 77 pseudobonds, 2087 residues, 7 models selected > transparency (#!3 & sel) 80 > select clear > show #!2 models > hide #!2 models > show #!1 models > hide #!3 models > select #1/3/7 4967 atoms, 5030 bonds, 3 pseudobonds, 638 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide sel cartoons > select #1/3/7/4 7424 atoms, 7517 bonds, 6 pseudobonds, 955 residues, 2 models selected > cartoon hide (#!1 & sel) > surface hidePatches (#!1 & sel) > show #!3 models > hide #!3 models > select #1/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516 741 atoms, 737 bonds, 102 residues, 1 model selected > color (#!1 & sel) red > select clear > select #1/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467 819 atoms, 821 bonds, 1 pseudobond, 112 residues, 2 models selected > color (#!1 & sel) light gray > select clear > select #1/5/2/4 7897 atoms, 8002 bonds, 6 pseudobonds, 1010 residues, 2 models selected > select #1/5/2/6 7919 atoms, 8029 bonds, 4 pseudobonds, 1012 residues, 2 models selected > transparency (#!1 & sel) 0 > select #1/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467 819 atoms, 821 bonds, 1 pseudobond, 112 residues, 2 models selected > transparency (#!1 & sel) 80 > select #1/2:633/3:499/4:658/5:506/6:665/7:550 54 atoms, 48 bonds, 6 residues, 1 model selected > select #1/3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516 741 atoms, 737 bonds, 102 residues, 1 model selected > transparency (#!1 & sel) 80 > select clear > lighting simple > select #1/5 2565 atoms, 2596 bonds, 2 pseudobonds, 330 residues, 2 models selected > ui tool show ""Color Actions"" > color (#!1 & sel) #228b22ff > select #1/5:500-516 123 atoms, 122 bonds, 17 residues, 1 model selected > transparency (#!1 & sel) 80 > select #1/5:448-467 155 atoms, 157 bonds, 20 residues, 1 model selected > transparency (#!1 & sel) 80 > select clear > select #1/6 2479 atoms, 2514 bonds, 1 pseudobond, 319 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide sel cartoons > show #!2 models > show #!3 models > hide #!2 models > hide #!3 models > select #1/ Expected an objects specifier or a keyword > surface (#!1 & sel) > select #1 17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 11 models selected > surface (#!1 & sel) > select #1/n/m Nothing selected > surface hidePatches #1 > select #1 17065 atoms, 17476 bonds, 10 pseudobonds, 2051 residues, 13 models selected > surface (#!1 & sel) > select x/y Expected an objects specifier or a keyword > select /x/y 3444 atoms, 3860 bonds, 168 residues, 2 models selected > show #!2 models > show #!3 models > select /x/y 3444 atoms, 3860 bonds, 168 residues, 2 models selected > surface hidePatches (#!1-2 & sel) > show sel cartoons > select /2 8610 atoms, 8740 bonds, 3 pseudobonds, 1087 residues, 6 models selected > ui tool show ""Color Actions"" > color (#!1-3 & sel) #00ff77ff > select /4 7678 atoms, 7776 bonds, 6 pseudobonds, 987 residues, 5 models selected > color (#!1-3 & sel) #b7ff9dff > select /6 7441 atoms, 7546 bonds, 3 pseudobonds, 957 residues, 5 models selected > color (#!1-3 & sel) #246b05ff > select /7 7654 atoms, 7753 bonds, 3 pseudobonds, 989 residues, 5 models selected > color (#!1-3 & sel) #6b8e23ff > select /3 7253 atoms, 7339 bonds, 6 pseudobonds, 931 residues, 6 models selected > color (#!1-3 & sel) #7fff00ff > select /5 7552 atoms, 7644 bonds, 5 pseudobonds, 975 residues, 6 models selected > color (#!1-3 & sel) #228b22ff > hide #!2 models > show #!2 models > select /3 7253 atoms, 7339 bonds, 6 pseudobonds, 931 residues, 6 models selected > surface hidePatches (#!1-3 & sel) > select > /3:493-509/7:544-560/4:652-668/6:659-675/2:627-643/5:500-516/3:441-460/7:492-511/4:600-619/6:607-626/2:575-594/5:448-467 4631 atoms, 4624 bonds, 3 pseudobonds, 636 residues, 5 models selected > show sel cartoons > transparency (#!1-3 & sel) 70 > select clear > hide cartoons > show cartoons > hide #!2 models > hide #!3 models > select /3 7253 atoms, 7339 bonds, 6 pseudobonds, 931 residues, 6 models selected > hide sel & #!1 cartoons > show #!2 models > hide #!1 models > select /3 7253 atoms, 7339 bonds, 6 pseudobonds, 931 residues, 6 models selected > hide sel & #!2 cartoons > show #!3 models > hide #!2 models > hide sel & #!3 cartoons > select /4/7 15332 atoms, 15529 bonds, 9 pseudobonds, 1976 residues, 6 models selected > surface (#!3 & sel) > show #!1 models > show #!2 models > hide #!2 models > hide #!3 models > select #1/5 2565 atoms, 2596 bonds, 2 pseudobonds, 330 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide sel cartoons > hide #!1 models > show #!3 models > select #3/5 2428 atoms, 2458 bonds, 1 pseudobond, 315 residues, 2 models selected > select #3/5 2428 atoms, 2458 bonds, 1 pseudobond, 315 residues, 2 models selected > select #3/7 2623 atoms, 2657 bonds, 1 pseudobond, 339 residues, 2 models selected > surface hidePatches (#!3 & sel) > hide sel cartoons > select #3/3/6 5010 atoms, 5076 bonds, 1 pseudobond, 646 residues, 2 models selected > surface hidePatches (#!3 & sel) > select #3/3/6/4 7728 atoms, 7831 bonds, 1 pseudobond, 994 residues, 2 models selected > surface hidePatches (#!3 & sel) > hide sel cartoons > show #!1 models > hide #!3 models > select #1/3/6/4 7306 atoms, 7400 bonds, 7 pseudobonds, 938 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide sel cartoons > select #1/3/6/4/7 9903 atoms, 10031 bonds, 7 pseudobonds, 1274 residues, 2 models selected > surface hidePatches (#!1 & sel) > hide sel cartoons > select #1/2/5 5440 atoms, 5515 bonds, 3 pseudobonds, 693 residues, 2 models selected > surface (#!1 & sel) > show sel cartoons > select clear > show #!2 models > hide #!2 models > show #!3 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!2 models > show #!3 models > hide #!1 models > hide #!3 models > select #2/3/6/4/7 9772 atoms, 9895 bonds, 9 pseudobonds, 1257 residues, 2 models selected > surface hidePatches (#!2 & sel) > hide sel cartoons > show #!1 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > hide #!1 models > save /Users/butryna/Desktop/image1.png supersample 3 > lighting full > lighting soft > lighting simple > lighting full ===== Log before crash end ===== Log: Startup Messages --- warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr bundle with that from OME-Zarr bundle Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 INTEL-22.5.11 OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine OpenGL vendor: Intel Inc. Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro16,2 Processor Name: Quad-Core Intel Core i5 Processor Speed: 2 GHz Number of Processors: 1 Total Number of Cores: 4 L2 Cache (per Core): 512 KB L3 Cache: 6 MB Hyper-Threading Technology: Enabled Memory: 16 GB System Firmware Version: 2022.140.5.0.0 (iBridge: 21.16.6074.0.0,0) OS Loader Version: 580.140.1~8 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 1 hour, 14 minutes Graphics/Displays: Intel Iris Plus Graphics: Chipset Model: Intel Iris Plus Graphics Type: GPU Bus: Built-In VRAM (Dynamic, Max): 1536 MB Vendor: Intel Device ID: 0x8a53 Revision ID: 0x0007 Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Framebuffer Depth: 30-Bit Color (ARGB2101010) Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 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: 2.10.5 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: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 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: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 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 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-ISOLDE: 1.7.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 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: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 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-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 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 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 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: 1.33.3 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: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 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: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Graphics nonchimerax all ChimeraX