id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20266 Crash in swap_buffers, Qt dispatched status line expose event during SideView makeCurrent() chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.11.1 (2026-01-23 05:51:34 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Bus error Current thread 0x0000000208d4b100 (most recent call first): File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 248 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 561 in swap_buffers File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 166 in status File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/statusbar.py"", line 98 in _expose_event File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 122 in make_current File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 555 in make_current File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 584 in use_shared_context File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 146 in render File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 115 in _redraw File ""/Applications/ChimeraX-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.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-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 169 in update_graphics_now File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 153 in resizeEvent File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/graphics.py"", line 61 in event File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 414 in event_loop File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX-1.11.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, 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unallocated=1.1G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= .note.gnu.proper 320 1 Accelerate framework 256K 2 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 976K 31 ColorSync 176K 11 CoreAnimation 4784K 150 CoreGraphics 32K 2 CoreServices 624K 2 CoreUI image data 5856K 52 Foundation 48K 2 Kernel Alloc Once 208K 3 MALLOC 422.9M 181 MALLOC guard page 3744K 4 Mach message 64K 3 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 720K 45 Stack 196.5M 46 Stack Guard 56.0M 1 VM_ALLOCATE 224.7M 227 VM_ALLOCATE (reserved) 256.0M 1 reserved VM address space (unallocated) __AUTH 5968K 656 __AUTH_CONST 90.5M 1042 __CTF 824 1 __DATA 42.9M 1138 __DATA_CONST 59.7M 1185 __DATA_DIRTY 8499K 899 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 619.8M 139 __OBJC_RO 78.4M 1 __OBJC_RW 2571K 1 __TEXT 1.5G 1172 __TEXT (graphics) 5360K 35 __TPRO_CONST 128K 2 dyld private memory 1584K 15 mapped file 636.8M 100 page table in kernel 1362K 1 shared memory 3680K 27 =========== ======= ======= TOTAL 4.2G 7187 TOTAL, minus reserved VM space 3.9G 7187 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""7c6d0237a244b78aebd7b5c9afd138b68be9d3f6"", ""bug_type"" : ""309"", ""roots_installed"" : 0, ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""67181b10c68c361a728c7cfa"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000005 }, { ""rolloutId"" : ""682ef9612c2ae30e2f38d3a4"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000006 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open pdb:1e3i Summary of feedback from opening 1e3i fetched from pdb --- notes | Fetching compressed mmCIF 1e3i from http://files.rcsb.org/download/1e3i.cif Fetching CCD CXF from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/F/CXF/CXF.cif Fetching CCD NAI from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/I/NAI/NAI.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif 1e3i title: Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more info...] Chain information for 1e3i #1 --- Chain | Description | UniProt A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376 Non-standard residues in 1e3i #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > open 1e3i fromDatabase pdb format mmcif 1e3i title: Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more info...] Chain information for 1e3i #2 --- Chain | Description | UniProt A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376 Non-standard residues in 1e3i #2 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > log metadata #2 Metadata for 1e3i #2 --- Title | Mouse class II alcohol dehydrogenase complex with NADH and inhibitor Citations | Svensson, S., Hoeoeg, J.O., Schneider, G., Sandalova, T. (2000). Crystal Structure of Mouse Class II Alcohol Dehydrogenase Reveal Determinants of Substrate Specificity and Catalytic Efficiency. J.Mol.Biol., 302, 441. PMID: 10970744. DOI: 10.1006/JMBI.2000.4039 Svensson, S., Stroemberg, P., Hoeoeg, J.O. (1999). A Novel Subtype of Class II Alcohol Dehydrogenase in Rodents. J.Biol.Chem., 274, 29712. PMID: 10514444. DOI: 10.1074/JBC.274.42.29712 Non-standard residues | CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion Gene source | Mus musculus (house mouse) Experimental method | X-ray diffraction Resolution | 2.100Å > hide cartoons > show cartoons > style stick Changed 12118 atom styles > style sphere Changed 12118 atom styles > style ball Changed 12118 atom styles > style stick Changed 12118 atom styles > show cartoons > show atoms > style sphere Changed 12118 atom styles > ui tool show ""Side View"" > view all > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 11898 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > style stick Changed 12118 atom styles > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > hide sel cartoons > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > hide sel cartoons > hide sel atoms > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > color (#!1 & sel) red > select add #2 9100 atoms, 8698 bonds, 25 pseudobonds, 1692 residues, 4 models selected > select subtract #2 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > select add #1 6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected > select subtract #1 Nothing selected > select add #2 6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected > select subtract #2 Nothing selected > select add #2 6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected > select subtract #2 Nothing selected > hide #!2 models > select add #1 6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected > select subtract #1 Nothing selected > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > show sel cartoons > show sel atoms > hide sel atoms > close #2 > close #1 > open pdb:1e3i format mmcif fromDatabase pdb 1e3i title: Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more info...] Chain information for 1e3i #1 --- Chain | Description | UniProt A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376 Non-standard residues in 1e3i #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > hide sel cartoons > show sel atoms > color sel red > color sel byelement Drag select of 1155 atoms, 3 pseudobonds, 1124 bonds > select clear > select /B:304 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:316 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select /A:324@CA 1 atom, 1 residue, 1 model selected > select /B:317 8 atoms, 7 bonds, 1 residue, 1 model selected > select /B:316 8 atoms, 7 bonds, 1 residue, 1 model selected Drag select of 2337 atoms, 8 pseudobonds, 2265 bonds > select clear > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 1 model selected > select down 2 atoms, 1 bond, 1 residue, 1 model selected > select down 1 bond, 1 model selected > select down 1 bond, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 1 model selected > select up 44 atoms, 47 bonds, 5 residues, 1 model selected > select up 2800 atoms, 2849 bonds, 376 residues, 1 model selected > select up 3041 atoms, 2906 bonds, 566 residues, 1 model selected > select down 2800 atoms, 2849 bonds, 376 residues, 1 model selected > select down 44 atoms, 47 bonds, 5 residues, 1 model selected > select down 4 atoms, 3 bonds, 1 residue, 1 model selected > select down 2 atoms, 1 bond, 1 residue, 1 model selected > select up 4 atoms, 3 bonds, 1 residue, 1 model selected > select add /A:181@C 5 atoms, 3 bonds, 2 residues, 1 model selected > select clear > select /B:308 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /A:318@C 1 atom, 1 residue, 1 model selected > label sel atoms attribute name > select up 4 atoms, 3 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select clear > close > open pdb:1e3i format mmcif fromDatabase pdb 1e3i title: Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more info...] Chain information for 1e3i #1 --- Chain | Description | UniProt A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376 Non-standard residues in 1e3i #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises.cxs"" > save /Users/ivana.kapustova/Desktop/image1.png supersample 3 > hide sel cartoons > hide sel atoms > show sel atoms > color (#!1 & sel) red > undo Undo failed, probably because structures have been modified. > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B Alignment identifier is 1 > select /A-B:95-96 32 atoms, 32 bonds, 4 residues, 1 model selected > select /A-B:95 14 atoms, 14 bonds, 2 residues, 1 model selected > sequence chain #1/A Alignment identifier is 1/A > select > /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375 695 atoms, 685 bonds, 92 residues, 1 model selected > select /A:75 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:75 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:75 6 atoms, 5 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select /A:235 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:235-238 28 atoms, 27 bonds, 4 residues, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select clear > undo > select /A:235-238 28 atoms, 27 bonds, 4 residues, 1 model selected > ~label sel residues > sequence chain #1/B Alignment identifier is 1/B > select > /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 947 atoms, 949 bonds, 128 residues, 1 model selected > select /B:235-236 14 atoms, 13 bonds, 2 residues, 1 model selected > select /B:235-238 28 atoms, 27 bonds, 4 residues, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > label sel attribute label_one_letter_code > select clear > select > /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 947 atoms, 949 bonds, 128 residues, 1 model selected > select /B:206-207 13 atoms, 12 bonds, 2 residues, 1 model selected > select /B:206-217 79 atoms, 78 bonds, 12 residues, 1 model selected > color sel cyan > select clear > select > /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375 695 atoms, 685 bonds, 92 residues, 1 model selected > select /A:316 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:316 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:316,351 13 atoms, 11 bonds, 2 residues, 1 model selected > color sel magenta > select > /A:46-52,100-105,119-123,169-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 972 atoms, 974 bonds, 131 residues, 1 model selected > select > /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375 695 atoms, 685 bonds, 92 residues, 1 model selected > select /A:246 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:246 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:351 5 atoms, 4 bonds, 1 residue, 1 model selected > select add /A:316 13 atoms, 11 bonds, 2 residues, 1 model selected > label sel attribute label_specifier > select clear > select /A:246 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:246 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:246,281 13 atoms, 11 bonds, 2 residues, 1 model selected > color sel purple > color sel forest green > label sel attribute label_specifier > select /A:4 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:4 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:4,39 13 atoms, 11 bonds, 2 residues, 1 model selected > color sel white > color sel blue > label sel attribute label_specifier > select /A:176 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:176 8 atoms, 7 bonds, 1 residue, 1 model selected > select > /A:46-52,100-105,119-123,169-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 972 atoms, 974 bonds, 131 residues, 1 model selected > select /A:176 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:176 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:176,211 13 atoms, 11 bonds, 2 residues, 1 model selected > color sel lime > color sel red > color sel orange > label sel attribute label_specifier > select clear > select /A:5,176,211 22 atoms, 19 bonds, 3 residues, 1 model selected > select clear > select /A:5 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:5 9 atoms, 8 bonds, 1 residue, 1 model selected > sequence chain #1/B Alignment identifier is 1/B > select /B:5 9 atoms, 8 bonds, 1 residue, 1 model selected > select /B:5 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select down 9 atoms, 8 bonds, 1 residue, 1 model selected > select down 9 atoms, 8 bonds, 1 residue, 1 model selected > select down 9 atoms, 8 bonds, 1 residue, 1 model selected > select clear > select /B:5@NZ 1 atom, 1 residue, 1 model selected > label sel atoms attribute name > label sel attribute label_one_letter_code > select clear > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises.cxs"" > select > /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 947 atoms, 949 bonds, 128 residues, 1 model selected > select > /B:7-14,22-28,35-44,63-64,68-76,88-91,134-136,139-141,153-157,161-164,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375 721 atoms, 710 bonds, 96 residues, 1 model selected > select > /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 947 atoms, 949 bonds, 128 residues, 1 model selected > select /B:47 7 atoms, 7 bonds, 1 residue, 1 model selected > select /B:47 7 atoms, 7 bonds, 1 residue, 1 model selected > select /B:47 7 atoms, 7 bonds, 1 residue, 1 model selected > select > /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 947 atoms, 949 bonds, 128 residues, 1 model selected > select clear > select /B:349 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:349 7 atoms, 6 bonds, 1 residue, 1 model selected > sequence chain #1/A Alignment identifier is 1/A > select > /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375 695 atoms, 685 bonds, 92 residues, 1 model selected > select /B:349 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:349 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:349-350 17 atoms, 17 bonds, 2 residues, 1 model selected > select /A:349-350 17 atoms, 17 bonds, 2 residues, 1 model selected > select > /A:7-13,22-28,35-44,68-76,88-91,134-136,139-141,153-157,161-163,198-202,222-226,243-245,268-271,292-295,302-306,315-318,348-353,371-375 695 atoms, 685 bonds, 92 residues, 1 model selected > select /A:349 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:349 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:349 7 atoms, 6 bonds, 1 residue, 1 model selected > select /B:349 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select > /B:46-52,100-105,119-123,172-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 947 atoms, 949 bonds, 128 residues, 1 model selected > select clear > select /B:349 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel atoms > ~label sel residues > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-PrimaryStructure.cxs"" > close session > open ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises.cxs"" format session > view name session-start opened ChimeraX session Drag select of 357 atoms, 749 residues, 17 pseudobonds, 304 bonds > close session > open pdb:1e3i format mmcif fromDatabase pdb 1e3i title: Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more info...] Chain information for 1e3i #1 --- Chain | Description | UniProt A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376 Non-standard residues in 1e3i #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > view > view all > select helix 1919 atoms, 1923 bonds, 259 residues, 1 model selected > color sel red > select clear > select strand 1416 atoms, 1395 bonds, 188 residues, 1 model selected > color sel purple > select up 5580 atoms, 5678 bonds, 749 residues, 1 model selected > select up 6059 atoms, 5792 bonds, 1126 residues, 1 model selected > select down 5580 atoms, 5678 bonds, 749 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select up 5580 atoms, 5678 bonds, 749 residues, 1 model selected > select up 6059 atoms, 5792 bonds, 1126 residues, 1 model selected > select up 6059 atoms, 5792 bonds, 1126 residues, 1 model selected > select up 6059 atoms, 5792 bonds, 1126 residues, 1 model selected > select down 5580 atoms, 5678 bonds, 749 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select down 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select strand 1416 atoms, 1395 bonds, 188 residues, 1 model selected > select coil 2245 atoms, 2238 bonds, 302 residues, 1 model selected > color sel white > select clear > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"" > color helix red > color helix orange > color helix red > ui tool show ""Show Sequence Viewer"" > sequence chain /A /B Alignment identifier is 1 > select /A-B:253 14 atoms, 14 bonds, 2 residues, 1 model selected > select /A-B:253-262 154 atoms, 154 bonds, 20 residues, 1 model selected > sequence chain #1/A Alignment identifier is 1/A > select clear > select /A:253-254 14 atoms, 14 bonds, 2 residues, 1 model selected > select /A:253-262 77 atoms, 77 bonds, 10 residues, 1 model selected > label sel attribute label_one_letter_code > show sel atoms > view sel > view > ui tool show ""Side View"" > view sel > ui tool show H-Bonds > cartoon suppressBackboneDisplay false > ui tool show H-Bonds > hbonds sel reveal true 29 hydrogen bonds found > view > select clear > select /A:371 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:371-375 41 atoms, 40 bonds, 5 residues, 1 model selected > color sel byelement > cartoon suppressBackboneDisplay false > view > view sel > cartoon suppressBackboneDisplay false > show sel atoms > ui tool show ""Side View"" > view > select /A:253 7 atoms, 7 bonds, 1 residue, 1 model selected > select /A:253-262 77 atoms, 77 bonds, 11 pseudobonds, 10 residues, 2 models selected > color (#!1 & sel) byelement > select /A:371 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:371-375 41 atoms, 40 bonds, 5 residues, 1 model selected > select sel @ show sel atoms > cartoon suppressBackboneDisplay false > show sel atoms > cartoon suppressBackboneDisplay false > color sel byelement > select clear > select /A:371 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:371-375 41 atoms, 40 bonds, 5 residues, 1 model selected > select sel: show sel atoms > color sel byelement > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"" > hide sel cartoons > hbonds sel reveal true 69 hydrogen bonds found > ui tool show H-Bonds > hbonds sel restrict both reveal true 32 hydrogen bonds found > hbonds sel reveal true 69 hydrogen bonds found > select clear > select /A:371 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:371-375 41 atoms, 40 bonds, 5 residues, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select clear > select /A:371 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:371-375 41 atoms, 40 bonds, 5 residues, 1 model selected > label sel attribute label_specifier > select clear > view > select /A:369 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:369 6 atoms, 5 bonds, 1 residue, 1 model selected > select /A:371 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:371-375 41 atoms, 40 bonds, 5 residues, 1 model selected > select strand 1416 atoms, 1395 bonds, 16 pseudobonds, 188 residues, 2 models selected > show sel cartoons > select clear > view Drag select of 817 atoms, 743 residues, 86 pseudobonds, 751 bonds > select clear > select /A:371 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:371-375 41 atoms, 40 bonds, 5 residues, 1 model selected > select sel: transparency 50,r #0 Missing or invalid ""percent"" argument: Expected a number > select transparency 50,r #0 Expected an objects specifier or a keyword > transparency sel 50 target c > select ~sel & ##selected 5856 atoms, 5594 bonds, 54 pseudobonds, 1100 residues, 3 models selected > transparency sel 50 target c > select clear > select > /A:46-52,100-105,119-123,169-189,205-218,229-239,246-250,253-262,275-285,307-312,320-339,343-346,356-366 972 atoms, 974 bonds, 3 pseudobonds, 131 residues, 2 models selected > select /A:253-254 14 atoms, 14 bonds, 2 residues, 1 model selected > select /A:253-262 77 atoms, 77 bonds, 10 residues, 1 model selected > select up 2800 atoms, 2849 bonds, 376 residues, 1 model selected > select down 77 atoms, 77 bonds, 10 residues, 1 model selected > hbonds sel reveal true 29 hydrogen bonds found > select /A:371 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:371-375 41 atoms, 40 bonds, 5 residues, 1 model selected > select sel: hbonds sel reveal true 69 hydrogen bonds found > select clear > select /A:349 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:349 7 atoms, 6 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select sel: hbonds sel reveal true 14 hydrogen bonds found > select clear > select /A:349 7 atoms, 6 bonds, 1 residue, 1 model selected > hbonds sel reveal true 3 hydrogen bonds found > select /A:371@O 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > label sel text ""{0.name} {0.number}{0.insertion_code}"" > select down 1 atom, 1 residue, 1 model selected > view sel > label sel atoms attribute name > select /A:349@OG1 1 atom, 1 residue, 1 model selected > select clear > select /A:349@N 1 atom, 1 residue, 1 model selected > label sel atoms attribute name > select /A:349 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select /A:349@O 1 atom, 1 residue, 1 model selected > label sel atoms attribute name > select clear > select /A:349@O 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > view > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"" > select /A:27 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:27 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > select sel: show sel atoms > color sel byelement > select /A:27 9 atoms, 8 bonds, 1 residue, 1 model selected > label sel text ""{0.label_one_letter_code} {0.number}{0.insertion_code}"" > select /A:27@O 1 atom, 1 residue, 1 model selected > select sel: select /A:23 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:23-32 79 atoms, 80 bonds, 10 residues, 1 model selected > select /A:24 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:24-31 62 atoms, 63 bonds, 8 residues, 1 model selected > show sel atoms > color sel byelement > select /A:27 9 atoms, 8 bonds, 1 residue, 1 model selected > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"" > undo > redo > undo > select sel: hide sel atoms > ~label sel residues > select clear > select /A:262@N 1 atom, 1 residue, 1 model selected > select /A:262@N 1 atom, 1 residue, 1 model selected > select /A:262 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:262 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:261 8 atoms, 7 bonds, 1 residue, 1 model selected > select /A:260 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:259 7 atoms, 6 bonds, 1 residue, 1 model selected > select /A:258 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > view > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"" > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:1-376 2800 atoms, 2849 bonds, 3 pseudobonds, 376 residues, 2 models selected > select ~sel & ##selected 3259 atoms, 2943 bonds, 17 pseudobonds, 750 residues, 2 models selected > hide sel atoms > hide sel cartoons > undo > select clear > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-SecondaryStructure.cxs"" > open ""/Users/ivana.kapustova/Library/CloudStorage/OneDrive- > KarolinskaInstitutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises.cxs"" > view name session-start opened ChimeraX session > close session > open pdb:1e3i format mmcif fromDatabase pdb 1e3i title: Mouse class II alcohol dehydrogenase complex with NADH and inhibitor [more info...] Chain information for 1e3i #1 --- Chain | Description | UniProt A B | ALCOHOL DEHYDROGENASE, CLASS II | Q9QYY9 1-376 Non-standard residues in 1e3i #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-TertiaryStructure.cxs"" > select chain 1/A Expected an objects specifier or a keyword > select chain1/A Expected an objects specifier or a keyword > select chainA Expected an objects specifier or a keyword > select chain A Expected an objects specifier or a keyword > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > select #1/A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > select ~sel & ##selected 3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected > hide sel atoms > hide sel cartoons > select /A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > hide sel atoms > select coil 2245 atoms, 2238 bonds, 302 residues, 1 model selected > select clear Drag select of 376 residues > ui tool show ""Color Actions"" > color sel bychain > color sel bypolymer > color sel bynucleotide > color sel byelement > color sel byhetero > color sel byhetero target c > color sel bychain target c > close session > open ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-TertiaryStructure.cxs"" > format session > view name session-start opened ChimeraX session > select /B 3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected > hide sel atoms > delete atoms (#!1 & sel) > delete bonds (#!1 & sel) > view > rainbow > select 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > hide sel atoms > select clear > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-TertiaryStructure.cxs"" > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > label sel atoms attribute name > label sel attribute label_specifier > select clear > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select /A:3 9 atoms, 8 bonds, 1 residue, 1 model selected > select /A:3-4 13 atoms, 12 bonds, 2 residues, 1 model selected > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > cartoon suppressBackboneDisplay false > ~label sel atoms > select /A:1@N 1 atom, 1 residue, 1 model selected > label sel atoms attribute name > select clear > select /A:376 12 atoms, 12 bonds, 1 residue, 1 model selected > select /A:376 12 atoms, 12 bonds, 1 residue, 1 model selected > cartoon suppressBackboneDisplay false > show sel atoms > select /A:376@N 1 atom, 1 residue, 1 model selected > select /A:376@N 1 atom, 1 residue, 1 model selected > label sel atoms attribute name > label sel attribute label_specifier > select clear Drag select of 7 residues > select /A:318 4 atoms, 3 bonds, 1 residue, 1 model selected > select add /A:317 12 atoms, 10 bonds, 2 residues, 1 model selected > select add /A:316 20 atoms, 17 bonds, 3 residues, 1 model selected > select add /A:315 26 atoms, 22 bonds, 4 residues, 1 model selected > select add /A:292 32 atoms, 27 bonds, 5 residues, 1 model selected > select add /A:293 38 atoms, 32 bonds, 6 residues, 1 model selected > select add /A:294 45 atoms, 38 bonds, 7 residues, 1 model selected > select add /A:295 52 atoms, 44 bonds, 8 residues, 1 model selected > select add /A:270 60 atoms, 51 bonds, 9 residues, 1 model selected > select add /A:271 68 atoms, 58 bonds, 10 residues, 1 model selected > select add /A:269 74 atoms, 63 bonds, 11 residues, 1 model selected > select add /A:268 86 atoms, 75 bonds, 12 residues, 1 model selected > select add /A:198 93 atoms, 81 bonds, 13 residues, 1 model selected > select add /A:199 99 atoms, 86 bonds, 14 residues, 1 model selected > select add /A:200 104 atoms, 90 bonds, 15 residues, 1 model selected > select add /A:201 111 atoms, 96 bonds, 16 residues, 1 model selected > select add /A:202 122 atoms, 107 bonds, 17 residues, 1 model selected > select add /A:225 127 atoms, 111 bonds, 18 residues, 1 model selected > select add /A:226 135 atoms, 118 bonds, 19 residues, 1 model selected > select add /A:224 143 atoms, 125 bonds, 20 residues, 1 model selected > select add /A:223 151 atoms, 132 bonds, 21 residues, 1 model selected > select add /A:222 162 atoms, 142 bonds, 22 residues, 1 model selected > select add /A:243 170 atoms, 149 bonds, 23 residues, 1 model selected > select add /A:244 176 atoms, 154 bonds, 24 residues, 1 model selected > select add /A:245 184 atoms, 161 bonds, 25 residues, 1 model selected > label sel text "" Parallel beta sheet"" > undo > redo > select /A:1@N 1 atom, 1 residue, 1 model selected > label sel atoms text ""N terminus"" > select /A:376@N 1 atom, 1 residue, 1 model selected > ~label sel atoms > select clear > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 12 atoms, 12 bonds, 1 residue, 1 model selected > color sel byelement > select /A:376@C 1 atom, 1 residue, 1 model selected > label sel atoms text ""C terminus"" > select clear > select add /A:243 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /A:244 14 atoms, 12 bonds, 2 residues, 1 model selected > select add /A:245 22 atoms, 19 bonds, 3 residues, 1 model selected > select add /A:222 33 atoms, 29 bonds, 4 residues, 1 model selected > select add /A:223 41 atoms, 36 bonds, 5 residues, 1 model selected > select add /A:224 49 atoms, 43 bonds, 6 residues, 1 model selected > select add /A:225 54 atoms, 47 bonds, 7 residues, 1 model selected > select add /A:226 62 atoms, 54 bonds, 8 residues, 1 model selected > select add /A:198 69 atoms, 60 bonds, 9 residues, 1 model selected > select add /A:199 75 atoms, 65 bonds, 10 residues, 1 model selected > select add /A:200 80 atoms, 69 bonds, 11 residues, 1 model selected > select add /A:201 87 atoms, 75 bonds, 12 residues, 1 model selected > select add /A:202 98 atoms, 86 bonds, 13 residues, 1 model selected > select add /A:268 110 atoms, 98 bonds, 14 residues, 1 model selected > select add /A:269 116 atoms, 103 bonds, 15 residues, 1 model selected > select add /A:270 124 atoms, 110 bonds, 16 residues, 1 model selected > select add /A:271 132 atoms, 117 bonds, 17 residues, 1 model selected > select add /A:292 138 atoms, 122 bonds, 18 residues, 1 model selected > select add /A:293 144 atoms, 127 bonds, 19 residues, 1 model selected > select add /A:294 151 atoms, 133 bonds, 20 residues, 1 model selected > select add /A:295 158 atoms, 139 bonds, 21 residues, 1 model selected > select add /A:315 164 atoms, 144 bonds, 22 residues, 1 model selected > select add /A:316 172 atoms, 151 bonds, 23 residues, 1 model selected > select add /A:317 180 atoms, 158 bonds, 24 residues, 1 model selected > select add /A:318 184 atoms, 161 bonds, 25 residues, 1 model selected > ~label sel residues > select clear > select /A:244 6 atoms, 5 bonds, 1 residue, 1 model selected > select add /A:224 14 atoms, 12 bonds, 2 residues, 1 model selected > select add /A:200 19 atoms, 16 bonds, 3 residues, 1 model selected > select add /A:269 25 atoms, 21 bonds, 4 residues, 1 model selected > select subtract /A:269 19 atoms, 16 bonds, 3 residues, 1 model selected > select add /A:270 27 atoms, 23 bonds, 4 residues, 1 model selected > select subtract /A:270 19 atoms, 16 bonds, 3 residues, 1 model selected > select add /A:269 25 atoms, 21 bonds, 4 residues, 1 model selected > select add /A:293 31 atoms, 26 bonds, 5 residues, 1 model selected > select add /A:316 39 atoms, 33 bonds, 6 residues, 1 model selected > label sel text ""Parallel beta sheet"" > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > color sel byelement > select clear > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > ~label sel residues > select /A:376 12 atoms, 12 bonds, 1 residue, 1 model selected > ~label sel residues > select clear > select add /A:339 8 atoms, 7 bonds, 1 residue, 1 model selected > select add /A:338 17 atoms, 15 bonds, 2 residues, 1 model selected > select add /A:337 29 atoms, 27 bonds, 3 residues, 1 model selected > select add /A:336 37 atoms, 34 bonds, 4 residues, 1 model selected > select add /A:335 43 atoms, 39 bonds, 5 residues, 1 model selected > select add /A:334 50 atoms, 45 bonds, 6 residues, 1 model selected > select add /A:333 58 atoms, 52 bonds, 7 residues, 1 model selected > select add /A:332 66 atoms, 59 bonds, 8 residues, 1 model selected > select add /A:331 73 atoms, 66 bonds, 9 residues, 1 model selected > select add /A:330 80 atoms, 72 bonds, 10 residues, 1 model selected > select add /A:329 86 atoms, 77 bonds, 11 residues, 1 model selected > select add /A:328 94 atoms, 84 bonds, 12 residues, 1 model selected > select add /A:327 101 atoms, 90 bonds, 13 residues, 1 model selected > select add /A:326 107 atoms, 95 bonds, 14 residues, 1 model selected > select add /A:325 116 atoms, 103 bonds, 15 residues, 1 model selected > save ""/Users/ivana.kapustova/OneDrive - Karolinska > Institutet/Teaching/Chemical > biology/2026_ChimeraX/savefiles/CanvasExercises-TertiaryStructure.cxs"" ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.11.1 (2026-01-23) © 2016-2025 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M2 Max OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.9.1, Qt 6.9.0 Qt runtime version: 6.9.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: Mac14,5 Model Number: Z17K000SYKS/A Chip: Apple M2 Max Total Number of Cores: 12 (8 Performance and 4 Efficiency) Memory: 64 GB System Firmware Version: 13822.81.10 OS Loader Version: 13822.81.10 Software: System Software Overview: System Version: macOS 26.3.1 (a) (25D771280a) Kernel Version: Darwin 25.3.0 Time since boot: 1 day, 6 hours, 11 minutes Graphics/Displays: Apple M2 Max: Chipset Model: Apple M2 Max Type: GPU Bus: Built-In Total Number of Cores: 30 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.12.1 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 25.4.0 babel: 2.17.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 3.12.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.4 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.1.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Animations: 1.0 ChimeraX-Aniso: 1.3.2 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.61.4 ChimeraX-AtomicLibrary: 14.2.1 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.3 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-Boltz: 1.1 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.2 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.6.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.0 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.11.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.5 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.4 ChimeraX-Dicom: 1.2.7 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.4 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5.3 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.4 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.7.3 ChimeraX-Label: 1.2 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.2 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.2.2 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.1.0 ChimeraX-MDcrds: 2.17.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.2 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.22 ChimeraX-ModelPanel: 1.6 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0.1 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.15.2 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.12 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.5 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.4 ChimeraX-ProfileGrids: 1.4.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.5 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.3 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.2 ChimeraX-Scenes: 0.3.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.3 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.10 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.17.3 ChimeraX-Shape: 1.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.1 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.49.1 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.5.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.5 ChimeraX-Zone: 1.0.1 click: 8.3.1 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.1.4 debugpy: 1.8.19 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.61.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.15.1 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.11 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 1.4.1 iniconfig: 2.3.0 ipykernel: 6.30.1 ipython: 9.5.0 ipython_pygments_lexers: 1.1.1 ipywidgets: 8.1.8 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.6.3 jupyter_core: 5.9.1 jupyterlab_widgets: 3.0.16 kiwisolver: 1.4.9 line_profiler: 5.0.0 lxml: 6.0.2 lz4: 4.3.2 Markdown: 3.8.2 MarkupSafe: 3.0.3 matplotlib: 3.10.7 matplotlib-inline: 0.2.1 mcp: 1.18.0 msgpack: 1.1.1 multidict: 6.7.0 ndindex: 1.10.1 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.14.1 numpy: 1.26.4 OpenMM: 8.2.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.5 pep517: 0.13.1 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 11.3.0 pip: 25.2 pkginfo: 1.12.1.2 platformdirs: 4.5.1 pluggy: 1.6.0 prompt_toolkit: 3.0.52 propcache: 0.4.1 psutil: 7.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pybind11: 3.0.1 pycollada: 0.8 pydantic: 2.12.5 pydantic-settings: 2.12.0 pydantic_core: 2.41.5 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.3.6 pynrrd: 1.0.0 PyOpenGL: 3.1.10 PyOpenGL-accelerate: 3.1.10 pyopenxr: 1.1.4501 pyparsing: 3.3.2 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.9.1 PyQt6-Qt6: 6.9.2 PyQt6-WebEngine-commercial: 6.9.0 PyQt6-WebEngine-Qt6: 6.9.2 PyQt6_sip: 13.10.2 pytest: 9.0.2 pytest-cov: 7.0.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.1 python-multipart: 0.0.21 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 4.1.0 roman-numerals-py: 4.1.0 rpds-py: 0.30.0 scipy: 1.14.0 setuptools: 80.9.0 sfftk-rw: 0.8.1 six: 1.17.0 snowballstemmer: 3.0.1 sortedcontainers: 2.4.0 soupsieve: 2.8.3 Sphinx: 8.2.3 sphinx-autodoc-typehints: 3.2.0 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 sse-starlette: 3.2.0 stack-data: 0.6.3 starlette: 0.52.1 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 1.5.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.4 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 urllib3: 2.6.3 uvicorn: 0.40.0 wcwidth: 0.3.2 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 widgetsnbextension: 4.0.15 yarl: 1.22.0 }}} " defect closed normal Window Toolkit can't reproduce all ChimeraX