id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 20265 Crash in swap_buffers exposing SideView during Mac wakeup, Qt 6.10 chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-26.3.1-arm64-arm-64bit ChimeraX Version: 1.12.dev202605010205 (2026-05-01 02:05:23 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 0x00000001f4f23100 (most recent call first): File ""/Applications/ChimeraX_Daily.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_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 564 in swap_buffers File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 202 in draw File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 310 in render File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/sideview/tool.py"", line 119 in exposeEvent File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 424 in event_loop File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1064 in init File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1229 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.pdb_lib._load_libs, chimerax.surface._surface, psutil._psutil_osx, psutil._psutil_posix, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imaging, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 55) 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unallocated=925.6M(94%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= .note.gnu.proper 320 1 Accelerate framework 128K 1 Activity Tracing 256K 1 AttributeGraph Data 1024K 1 CG image 6160K 53 CG raster data 3296K 7 ColorSync 128K 8 CoreAnimation 3104K 163 CoreGraphics 48K 3 CoreGraphics (reserved) 16K 1 reserved VM address space (unallocated) CoreUI image data 3088K 33 Dispatch continuations 64.0M 1 Foundation 48K 2 Kernel Alloc Once 48K 2 MALLOC 318.2M 103 MALLOC guard page 3344K 4 Mach message 64K 2 OpenGL GLSL 256K 3 PROTECTED_MEMORY 16K 1 STACK GUARD 656K 41 Stack 209.4M 42 Stack Guard 56.0M 1 VM_ALLOCATE 225.2M 230 VM_ALLOCATE (reserved) 160.0M 2 reserved VM address space (unallocated) __AUTH 5968K 656 __AUTH_CONST 90.5M 1041 __CTF 824 1 __DATA 42.7M 1131 __DATA_CONST 60.6M 1180 __DATA_DIRTY 8499K 899 __FONT_DATA 2352 1 __GLSLBUILTINS 5176K 1 __INFO_FILTER 8 1 __LINKEDIT 618.7M 135 __OBJC_RO 78.4M 1 __OBJC_RW 2571K 1 __TEXT 1.5G 1202 __TPRO_CONST 128K 2 dyld private memory 1456K 13 mapped file 341.1M 87 page table in kernel 1205K 1 shared memory 3200K 28 =========== ======= ======= TOTAL 3.8G 7087 TOTAL, minus reserved VM space 3.6G 7087 "", ""legacyInfo"" : { ""threadTriggered"" : { ""name"" : ""CrBrowserMain"", ""queue"" : ""com.apple.main-thread"" } }, ""logWritingSignature"" : ""f02a4fbb8015e349852ed4bb39ca8c3b27a20e01"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""trmStatus"" : 1, ""trialInfo"" : { ""rollouts"" : [ { ""rolloutId"" : ""64c17a9925d75a7281053d4c"", ""factorPackIds"" : [ ""64d29746ad29a465b3bbeace"" ], ""deploymentId"" : 240000002 }, { ""rolloutId"" : ""67648e5334a82511f4acf879"", ""factorPackIds"" : [ ], ""deploymentId"" : 240000008 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== UCSF ChimeraX version: 1.12.dev202605010205 (2026-05-01) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/chiaramcallister/Downloads/1E3I.pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > view sel > lighting simple > lighting shadows true > lighting simple > ui tool show ""Selection Inspector"" > set bgColor white > set bgColor black > lighting simple > select add #1 6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected > select subtract #1 Nothing selected > show cartoons > color bynucleotide > view > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > view sel > view > cartoon > color red strands false Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color cyan strands Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color red helices Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color yellow coils Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color red :/isHelix Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color cyan :/isStrand Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color yellow :/isCoil Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > hide atoms > show cartoons > color byss Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select helix 1919 atoms, 1923 bonds, 259 residues, 1 model selected > color red sel Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel red > hide atoms > cartoon > color all yellow > select helix 1919 atoms, 1923 bonds, 259 residues, 1 model selected > color sel red > select strand 1416 atoms, 1395 bonds, 188 residues, 1 model selected > color sel cyan > select clear > view > view orient Drag select of 41 residues > style sel stick Changed 324 atom styles > style sel stick Changed 324 atom styles > color sel magenta > show sel atoms > style sel stick Changed 324 atom styles > label sel residues > style sel stick Changed 324 atom styles > style sel stick Changed 324 atom styles > clear Unknown command: clear > hide atoms > cartoon > select clear > hide atoms > cartoon > color bychain > hide names\ Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide names\ Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > label delete > select /A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > view sel > rainbow sel > color /A:1-120 blue > color /A:121-249 orange > color /A:250-376 blue > hide /B cartoons > N-terminus: blue → green → yellow → orange → red: C-terminus Unknown command: N-terminus: blue → green → yellow → orange → red: C-terminus > rainbow sel > select :NAI 88 atoms, 96 bonds, 2 residues, 1 model selected > show sel atoms > style sel ball Changed 88 atom styles > sequence chain #1/A Alignment identifier is 1/A > select /A:1 4 atoms, 3 bonds, 1 residue, 1 model selected > select /A:1-128 964 atoms, 984 bonds, 128 residues, 1 model selected > lighting simple > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel cartoons > show sel cartoons > ui tool show ""Selection Inspector"" > select /A:1-120 898 atoms, 918 bonds, 120 residues, 1 model selected > color sel white > select /A:250-376 955 atoms, 970 bonds, 127 residues, 1 model selected > color sel white > show /A cartoons > color /A rainbow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select clear > rainbow > color /A rainbow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select /A:1-180 color sel white Expected a keyword > select /A:1-180 1371 atoms, 1398 bonds, 180 residues, 1 model selected > color sel white > select /A:320-376 458 atoms, 468 bonds, 57 residues, 1 model selected > color sel white > rainbow sel > select clear > rainbow > /A:181-319 Unknown command: /A:181-319 > color sel white > select /A:181-319 971 atoms, 981 bonds, 139 residues, 1 model selected > color sel white > color /A rainbow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select /A:1-180,320-376 1829 atoms, 1866 bonds, 237 residues, 1 model selected > color sel white > rainbow sel > select clear > rainbow > color /A rainbow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select /A:1-180,320-376 1829 atoms, 1866 bonds, 237 residues, 1 model selected > color sel white > color /A rainbow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select /A:1-120,250-376 1853 atoms, 1888 bonds, 247 residues, 1 model selected > color sel white > rainbow sel > select clear > rainbow > select /A:1-180,320-376 1829 atoms, 1866 bonds, 237 residues, 1 model selected > cartoon > color bychain > hbonds /A restrict /B reveal true 50 hydrogen bonds found > select clear > show atoms > hide atoms > color all gray > select helix 1919 atoms, 1923 bonds, 259 residues, 1 model selected > color sel red > select strand 1416 atoms, 1395 bonds, 6 pseudobonds, 188 residues, 2 models selected > color sel cyan > select clear > hide atoms > cartoon > color bychain > hide atoms > cartoon > color bychain > select /A & /B around 4 Expected a keyword > select add /B & /A around 4 Expected a keyword > hbonds /A & /B around 4 reveal true Expected a keyword > hbonds reveal true 1627 hydrogen bonds found > hbonds hide true Expected a keyword > hbonds hide Expected a keyword > hbonds hide Expected a keyword > hidehbonds Unknown command: hidehbonds > hide hbonds > select /A & : select /A & : select /A & : hbonds /A restrict /B reveal true 50 hydrogen bonds found > select :ZN 4 atoms, 4 residues, 1 model selected > show sel atoms > style sel sphere Changed 4 atom styles > label sel residues > color sel residues Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel residues white Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel rwhite Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel white > select sel zr label sel residues > show sel atoms > style sel stick Changed 4 atom styles > select zone sel 3 Selected 18 atoms, 1 surfaces > show sel atoms > style sel stick Changed 18 atom styles > label sel residues > distance sel Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 18 atoms and 0 measurable objects > select zn Expected an objects specifier or a keyword > select zn381 Expected an objects specifier or a keyword > select /A:ZN 2 atoms, 2 residues, 1 model selected > select zone sel 2.6 Selected 8 atoms, 1 surfaces > distance sel & :ZN sel & ~:ZN Expected a keyword > distance :ZN & sel, ~:ZN & sel Expected a keyword > select /A:ZN 2 atoms, 2 residues, 1 model selected > name zn ""zn"" is not defined > select zone zn 2.6 Missing or invalid ""near"" argument: invalid objects specifier > select sel & ~zn Expected a keyword > name near ""near"" is not defined > distance zn, near Missing or invalid ""objects"" argument: invalid objects specifier > distance /A:ZN /A:46@SG Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 3 atoms and 0 measurable objects > distance /A:ZN /A:67@NE2 Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 3 atoms and 0 measurable objects > distance /A:ZN /A:178@SG Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 3 atoms and 0 measurable objects > select /A:ZN 2 atoms, 2 residues, 1 model selected > label sel atoms > distance /A:380@ZN /A:46@SG Distance between /A ZN 380 ZN and CYS 46 SG: 2.305Å > distance /A:380@ZN /A:67@NE2 Distance between /A ZN 380 ZN and HIS 67 NE2: 2.196Å > distance /A:380@ZN /A:174@SG Distance between /A ZN 380 ZN and CYS 174 SG: 12.244Å > show target m > distance /A:380@ZN /A:178@SG Distance between /A ZN 380 ZN and CYS 178 SG: 2.287Å > distance /A:381@ZN /A:97@SG distance /A:381@ZN /A:100@SG distance /A:381@ZN > /A:103@SG distance /A:381@ZN /A:111@SG Expected a keyword > distance /A:381@ZN /A:97@SGS Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 1 atoms and 0 measurable objects > distance /A:381@ZN /A:97@SG Distance between /A ZN 381 ZN and CYS 97 SG: 2.312Å > distance /A:381@ZN /A:100@SG Distance between /A ZN 381 ZN and CYS 100 SG: 2.306Å > distance /A:381@ZN /A:103@SG Distance between /A ZN 381 ZN and CYS 103 SG: 2.287Å > distance /A:381@ZN /A:111@SG Distance between /A ZN 381 ZN and CYS 111 SG: 2.299Å > delete /B > clear sel Unknown command: clear sel > select clear > select :NAI 44 atoms, 48 bonds, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 44 atom styles > color sel byelement > view sel > select zone sel 4 protein residues true Selected 188 atoms > show sel atoms > style sel stick Changed 188 atom styles > color sel byelement > hbonds sel reveal true 73 hydrogen bonds found > select :NAI@C4N 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel magenta > style sel ball Changed 1 atom style > select zone sel 3 protein residues true Selected 6 atoms > ~hbonds > ~distances Unknown command: ~distances > ~distance > ~zn Unknown command: ~zn > hide atoms > hide cartoons > show :NAI atoms > show :CXF atoms > style :NAI stick Changed 44 atom styles > style :CXF stick Changed 9 atom styles > color :NAI byelement > color :CXF byelement > close session > open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > delete /B > color byelement > show :NAI atoms > show :CXF atoms > style :NAI stick Changed 44 atom styles > style :CXF stick Changed 9 atom styles > color :NAI byelement > color :CXF byelement > select :NAI 44 atoms, 48 bonds, 1 residue, 1 model selected > select zone sel 3.5 protein residues true Selected 128 atoms > show sel atoms > style sel stick Changed 128 atom styles > color sel byelement > label sel residues > view sel > hbonds sel restrict cross reveal true 59 hydrogen bonds found > ui mousemode right zoom > ~select atoms > select subtract atoms Expected an objects specifier or a keyword > ~struts sel atoms > struts delete sel atoms Missing ""atoms"" keyword's argument > hide sel atoms > ui mousemode right select > select /A:377@C2N 1 atom, 1 residue, 1 model selected > select /A:377@C4N 1 atom, 1 residue, 1 model selected > style sel ball Changed 1 atom style > hide residues Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide atoms > show atoms\ Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > show atoms > ~atoms Unknown command: ~atoms > ~struts atoms > struts delete atoms Missing ""atoms"" keyword's argument > ~struts atoms > struts delete atoms Missing ""atoms"" keyword's argument > hide atoms > hide residdues Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide residues Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide bonds > hide hbonds > select /A:377@C4N 1 atom, 1 residue, 1 model selected > select :NAI 44 atoms, 48 bonds, 1 residue, 1 model selected > select zone sel 3.5 protein residues true Selected 128 atoms > show :NAI atoms > style :NAI stick Changed 44 atom styles > color :NAI byelement > show :NAI atoms > style :NAI stick Changed 44 atom styles > color :NAI byelement > style :NAI ball stick Expected a keyword > style :NAI ball-and-stick Expected a keyword > stylw :NAI ball-and-stick Unknown command: stylw :NAI ball-and-stick > style:NAI ball-and-stick Unknown command: style:NAI ball-and-stick > style :NAI ball-and-stick Expected a keyword > style :NAI ball Changed 44 atom styles > show :NAI atoms > style :NAI ball-and-stick Expected a keyword > color :NAI byelement > close session > open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > hide /B > delete /B > hide atoms > hide cartoons > show :NAI atoms > style :NAI ball-and-stick Expected a keyword > color :NAI byelement > view :NAI > select :NAI@C4N 1 atom, 1 residue, 1 model selected > show sel atoms > style sel sphere Changed 1 atom style > color sel magenta > label sel atoms > view sel > style sel ball Changed 1 atom style > select :NAI@C4N 1 atom, 1 residue, 1 model selected > select zone sel 4 protein residues true Selected 6 atoms > show sel atoms > style sel stick Changed 6 atom styles > color sel byelement > label sel residues > view sel > select :NAD Nothing selected > show sel > style sel stick Changed 0 atom styles > hide protein > select protein & within 4 of :NAD Expected a keyword > show sel > select protein & within 4 of sel Expected a keyword > select protein & within 4 of sel Expected a keyword > select protein & (within 4 of :NAD) Expected a keyword > hide > show :NAD > style :NAD stick Changed 0 atom styles > zone :NAD 4 Expected a keyword > zone :NAD show ligand > style ligand stick Changed 53 atom styles > contacts ligand protein Expected a keyword > show atoms > select sel @ select :NAD Nothing selected > select ligand 53 atoms, 57 bonds, 2 residues, 1 model selected > select clear > view > select :NAD Nothing selected > show sel > style sel stick Changed 0 atom styles > hide protein > hide atoms] Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide atoms] Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > close session > open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > delete /B > hide protein > select main 2800 atoms, 2849 bonds, 376 residues, 1 model selected > hide sel > view sel > view > delete sel > select ligand 53 atoms, 57 bonds, 2 residues, 1 model selected > select sel @ show sel > hbonds sel reveal true 11 hydrogen bonds found > view sel > show protein > close session > open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > select :NAD Nothing selected > show sel > style sel stick Changed 0 atom styles > view > hide /B > select :NAD show sel Expected a keyword > close session > open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > select ((/A & ::polymer_type>0 ) & ((/B & ::polymer_type>0 ) :0 ) & ((/A & ::polymer_type>0 ) : select clear > select ligand 106 atoms, 114 bonds, 4 residues, 1 model selected > select sel : show sel > hide ~ sel > view sel > hide /B > delete /B > view sel Drag select of 5 atoms, 14 residues, 4 bonds > select ligand 53 atoms, 57 bonds, 2 residues, 1 model selected > hbonds sel reveal true 23 hydrogen bonds found > select sel : hide ~sel > hide > undo > hide > show sel > hide > hide protein > select /A 3041 atoms, 2906 bonds, 31 pseudobonds, 566 residues, 3 models selected > hide > delete Missing or invalid ""atoms"" argument: empty atom specifier > delete /A > open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > hide /A > hide /A ?B Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide /B > select /A 3041 atoms, 2906 bonds, 8 pseudobonds, 566 residues, 2 models selected > hide /B > hide #!1 models > show #!1 models > hide /B > hide #!1 target m > show #!1 models > select add #1 6059 atoms, 5792 bonds, 17 pseudobonds, 1126 residues, 2 models selected > select subtract #1 Nothing selected > hide #1.1 models > show #1.1 target m > hide #1.1 models > select /B 3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected > hide /sel > select ::name=""NAI"" 88 atoms, 96 bonds, 2 residues, 1 model selected > show sel atoms > select sel : show sel atoms > style sel ball Changed 372 atom styles > style sel stick Changed 372 atom styles > color sel byelement > select ::name=""NAI"" 88 atoms, 96 bonds, 2 residues, 1 model selected > style sel ball Changed 88 atom styles > hide /sel > hide /B > hide /chainB > select /B 3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected > hide sel cartoons > select ::name=""NAI"" 88 atoms, 96 bonds, 2 residues, 1 model selected > select sel : select sel : 3.5 & ~sel Nothing selected > hide cartoons > hbonds reveal true 1627 hydrogen bonds found > ~hbonds > select ligand 106 atoms, 114 bonds, 4 residues, 1 model selected > select /B 3018 atoms, 2886 bonds, 11 pseudobonds, 560 residues, 3 models selected > hide sel atoms > select /ligand Nothing selected > select ::name=""NAI"" 88 atoms, 96 bonds, 2 residues, 1 model selected > select sel :> 3.5 & ~sel 5687 atoms, 5399 bonds, 14 pseudobonds, 1071 residues, 3 models selected > hide sel atoms > hide #* target a > show (#!1 & sel) target ab > undo > select ::name=""NAI"" 88 atoms, 96 bonds, 2 residues, 1 model selected > show sel atoms > delete /B > select sel : style sel stick Changed 143 atom styles > show sel atoms > hbonds sel reveal true 78 hydrogen bonds found > undo > view sel No displayed objects specified. > select ::name=""NAI"" 44 atoms, 48 bonds, 1 residue, 1 model selected > hbonds sel reveal true 21 hydrogen bonds found > close session > open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > fetch3cos Unknown command: fetch3cos > fetch 3cos Unknown command: fetch 3cos Select a database from the database table > open 3cos fromDatabase pdbe_bio format mmcif Summary of feedback from opening 3cos fetched from pdbe_bio --- warnings | Missing or incorrect sequence information. Inferred polymer connectivity. Missing or incorrect sequence information. Inferred polymer connectivity. notes | Fetching compressed 3cos bioassembly 1 from https://www.ebi.ac.uk/pdbe/static/entry/download/3cos-assembly-1.cif.gz Fetching CCD ACY from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/Y/ACY/ACY.cif Fetching CCD EDO from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/O/EDO/EDO.cif Fetching CCD NAD from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/D/NAD/NAD.cif Fetching CCD ZN from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/N/ZN/ZN.cif Fetching compressed 3cos bioassembly 2 from https://www.ebi.ac.uk/pdbe/static/entry/download/3cos-assembly-2.cif.gz 3cos bioassembly 1 title: Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex with NAD and Zn [more info...] 3cos bioassembly 1 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly Chain information for 3cos bioassembly 1 #2.1 --- Chain | Description A B | Alcohol dehydrogenase 4 Non-standard residues in 3cos bioassembly 1 #2.1 --- ACY — (ACY) EDO — (EDO) NAD — (NAD) ZN — (ZN) 3cos bioassembly 2 title: Crystal structure of human class II alcohol dehydrogenase (ADH4) in complex with NAD and Zn [more info...] 3cos bioassembly 2 mmCIF Assemblies --- 1| author_and_software_defined_assembly 2| author_and_software_defined_assembly 12 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. Chain information for 3cos bioassembly 2 #2.2 --- Chain | Description C | Alcohol dehydrogenase 4 D | Alcohol dehydrogenase 4 Non-standard residues in 3cos bioassembly 2 #2.2 --- ACY — (ACY) EDO — (EDO) NAD — (NAD) ZN — (ZN) Opened 2 biological assemblies for 3cos Computing secondary structure > hide #!1 models > hide #!2 models > show #!2 models > view > hide #2.2 models > show #2.2 models > show #!1 models > select #2.2/C 2789 atoms, 2840 bonds, 379 residues, 1 model selected > hide sel > hide /sel > hide sel cartoons > select #2.2/D 2802 atoms, 2853 bonds, 381 residues, 1 model selected > hide sel cartoons > ui tool show Matchmaker > matchmaker #2.1/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 1E3I.pdb, chain A (#1) with 3cos bioassembly 1, chain A (#2.1), sequence alignment score = 1563.8 RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs: 1.032) > matchmaker #2.1/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 1E3I.pdb, chain A (#1) with 3cos bioassembly 1, chain A (#2.1), sequence alignment score = 1563.8 RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs: 1.032) > select ::name=""THR"" 1127 atoms, 970 bonds, 161 residues, 3 models selected > select :48 54 atoms, 52 bonds, 6 residues, 3 models selected Drag select of 75 residues, 6 atoms, 4 bonds > undo > view sel Drag select of 344 atoms, 322 bonds Drag select of 123 atoms, 116 bonds Drag select of 390 atoms, 362 bonds > delete sel > view > select :48.A Expected an objects specifier or a keyword > select :48 44 atoms, 42 bonds, 5 residues, 3 models selected > view sel > ui tool show ""Side View"" > view orient Drag select of 6 atoms, 16 residues, 4 bonds > undo Drag select of 23 residues, 3 atoms, 3 bonds > ui mousemode right rotate > ui mousemode right translate > undo > select sel :> 3.5 17318 atoms, 16486 bonds, 33 pseudobonds, 3284 residues, 5 models selected > delete sel > select :48 44 atoms, 42 bonds, 5 residues, 3 models selected > ui mousemode right select Drag select of 146 atoms, 15 residues, 145 bonds, 3 pseudobonds > hbonds sel reveal true 57 hydrogen bonds found > select clear > ~hbonds > open /Users/chiaramcallister/Downloads/3COS.pdb 3COS.pdb title: Crystal structure of human class II alcohol dehydrogenase (ADH4) In complex with nad and Zn [more info...] Chain information for 3COS.pdb #3 --- Chain | Description | UniProt A B C D | alcohol dehydrogenase class II π chain | ADH4_HUMAN 1-380 Non-standard residues in 3COS.pdb #3 --- ACY — acetic acid EDO — 1,2-ethanediol (ethylene glycol) NAD — nicotinamide-adenine-dinucleotide ZN — zinc ion 12 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > close session > open /Users/chiaramcallister/Downloads/1E3I.pdb format pdb 1E3I.pdb title: Mouse class II alcohol dehydrogenase complex with nadh and inhibitor [more info...] Chain information for 1E3I.pdb #1 --- Chain | Description | UniProt A B | alcohol dehydrogenase, class II | Q9QYY9 1-376 Non-standard residues in 1E3I.pdb #1 --- CXF — cyclohexylformamide NAI — 1,4-dihydronicotinamide adenine dinucleotide (NADH) ZN — zinc ion > open /Users/chiaramcallister/Downloads/3COS.pdb 3COS.pdb title: Crystal structure of human class II alcohol dehydrogenase (ADH4) In complex with nad and Zn [more info...] Chain information for 3COS.pdb #2 --- Chain | Description | UniProt A B C D | alcohol dehydrogenase class II π chain | ADH4_HUMAN 1-380 Non-standard residues in 3COS.pdb #2 --- ACY — acetic acid EDO — 1,2-ethanediol (ethylene glycol) NAD — nicotinamide-adenine-dinucleotide ZN — zinc ion 12 atoms have alternate locations. Control/examine alternate locations with Altloc Explorer [start tool...] or the altlocs command. > select :48 54 atoms, 52 bonds, 6 residues, 2 models selected > ui tool show Matchmaker > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 1E3I.pdb, chain A (#1) with 3COS.pdb, chain A (#2), sequence alignment score = 1563.8 RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs: 1.032) > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 1E3I.pdb, chain A (#1) with 3COS.pdb, chain A (#2), sequence alignment score = 1563.8 RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs: 1.032) > matchmaker #2/A to #1/A pairing ss Parameters --- Chain pairing | ss 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 1E3I.pdb, chain A (#1) with 3COS.pdb, chain A (#2), sequence alignment score = 1563.8 RMSD between 363 pruned atom pairs is 0.675 angstroms; (across all 376 pairs: 1.032) > select #2/C 3040 atoms, 2894 bonds, 8 pseudobonds, 581 residues, 2 models selected > hide sel > hide sel cartoons > select #2/D 3047 atoms, 2910 bonds, 8 pseudobonds, 574 residues, 2 models selected > hide sel cartoons > select clear > select :48 54 atoms, 52 bonds, 6 residues, 2 models selected > select sel :> 3.5 17575 atoms, 16749 bonds, 36 pseudobonds, 3334 residues, 4 models selected > hide sel cartoons > hide sel atoms > select #1/B 3018 atoms, 2886 bonds, 9 pseudobonds, 560 residues, 2 models selected > hide sel > hide sel cartoons > select #2/B 2995 atoms, 2893 bonds, 8 pseudobonds, 537 residues, 2 models selected > hide sel cartoons > hide sel atoms > hide sel surfaces Drag select of 52 atoms, 56 bonds > select clear > select :48 54 atoms, 52 bonds, 6 residues, 2 models selected > select clear > select :48 54 atoms, 52 bonds, 6 residues, 2 models selected > select sel : show sel > select sel : show sel > select :48 54 atoms, 52 bonds, 6 residues, 2 models selected > view sel Drag select of 40 atoms, 4 residues, 38 bonds > select :48 54 atoms, 52 bonds, 6 residues, 2 models selected > ui mousemode right ""translate selected models"" > view matrix models > #1,1,0,0,-0.57062,0,1,0,1.0709,0,0,1,-0.184,#2,-0.97764,0.13032,0.16502,60.643,-0.19865,-0.8297,-0.52167,126.97,0.068938,-0.54279,0.83703,13.217 > view matrix models > #1,1,0,0,1.0187,0,1,0,0.37111,0,0,1,2.3508,#2,-0.97764,0.13032,0.16502,62.232,-0.19865,-0.8297,-0.52167,126.27,0.068938,-0.54279,0.83703,15.752 > view matrix models > #1,1,0,0,4.4031,0,1,0,-2.8243,0,0,1,7.6286,#2,-0.97764,0.13032,0.16502,65.616,-0.19865,-0.8297,-0.52167,123.08,0.068938,-0.54279,0.83703,21.03 > view matrix models > #1,1,0,0,6.3148,0,1,0,-3.9021,0,0,1,11.132,#2,-0.97764,0.13032,0.16502,67.528,-0.19865,-0.8297,-0.52167,122,0.068938,-0.54279,0.83703,24.534 > view matrix models > #1,1,0,0,5.7578,0,1,0,-2.9656,0,0,1,13.067,#2,-0.97764,0.13032,0.16502,66.971,-0.19865,-0.8297,-0.52167,122.94,0.068938,-0.54279,0.83703,26.468 > view matrix models > #1,1,0,0,5.1394,0,1,0,-1.8949,0,0,1,15.557,#2,-0.97764,0.13032,0.16502,66.353,-0.19865,-0.8297,-0.52167,124.01,0.068938,-0.54279,0.83703,28.958 > view matrix models > #1,1,0,0,3.5394,0,1,0,0.5167,0,0,1,18.05,#2,-0.97764,0.13032,0.16502,64.753,-0.19865,-0.8297,-0.52167,126.42,0.068938,-0.54279,0.83703,31.452 > view matrix models > #1,1,0,0,-2.6756,0,1,0,2.5741,0,0,1,15.921,#2,-0.97764,0.13032,0.16502,58.538,-0.19865,-0.8297,-0.52167,128.48,0.068938,-0.54279,0.83703,29.322 > view matrix models > #1,1,0,0,-6.0326,0,1,0,2.0178,0,0,1,13.12,#2,-0.97764,0.13032,0.16502,55.181,-0.19865,-0.8297,-0.52167,127.92,0.068938,-0.54279,0.83703,26.521 > view matrix models > #1,1,0,0,-7.0317,0,1,0,1.1619,0,0,1,11.603,#2,-0.97764,0.13032,0.16502,54.182,-0.19865,-0.8297,-0.52167,127.07,0.068938,-0.54279,0.83703,25.005 > view matrix models > #1,1,0,0,-7.8944,0,1,0,0.60728,0,0,1,13.615,#2,-0.97764,0.13032,0.16502,53.319,-0.19865,-0.8297,-0.52167,126.51,0.068938,-0.54279,0.83703,27.016 > view matrix models > #1,1,0,0,-9.5228,0,1,0,-0.60241,0,0,1,17.751,#2,-0.97764,0.13032,0.16502,51.69,-0.19865,-0.8297,-0.52167,125.3,0.068938,-0.54279,0.83703,31.153 > view matrix models > #1,1,0,0,-9.879,0,1,0,-2.2451,0,0,1,21.527,#2,-0.97764,0.13032,0.16502,51.334,-0.19865,-0.8297,-0.52167,123.66,0.068938,-0.54279,0.83703,34.928 > view matrix models > #1,1,0,0,-8.7981,0,1,0,-2.8785,0,0,1,21.773,#2,-0.97764,0.13032,0.16502,52.415,-0.19865,-0.8297,-0.52167,123.02,0.068938,-0.54279,0.83703,35.174 > view matrix models > #1,1,0,0,-11.782,0,1,0,-8.2767,0,0,1,19.794,#2,-0.97764,0.13032,0.16502,49.431,-0.19865,-0.8297,-0.52167,117.63,0.068938,-0.54279,0.83703,33.195 > view matrix models > #1,1,0,0,-10.617,0,1,0,-8.6174,0,0,1,19.963,#2,-0.97764,0.13032,0.16502,50.596,-0.19865,-0.8297,-0.52167,117.29,0.068938,-0.54279,0.83703,33.365 > view matrix models > #1,1,0,0,-11.145,0,1,0,-8.436,0,0,1,20.081,#2,-0.97764,0.13032,0.16502,50.068,-0.19865,-0.8297,-0.52167,117.47,0.068938,-0.54279,0.83703,33.482 > view matrix models > #1,1,0,0,-13.623,0,1,0,-4.677,0,0,1,19.748,#2,-0.97764,0.13032,0.16502,47.59,-0.19865,-0.8297,-0.52167,121.23,0.068938,-0.54279,0.83703,33.149 > view matrix models > #1,1,0,0,-10.698,0,1,0,-3.5663,0,0,1,22.647,#2,-0.97764,0.13032,0.16502,50.516,-0.19865,-0.8297,-0.52167,122.34,0.068938,-0.54279,0.83703,36.048 > view matrix models > #1,1,0,0,-9.455,0,1,0,-5.0995,0,0,1,18.67,#2,-0.97764,0.13032,0.16502,51.758,-0.19865,-0.8297,-0.52167,120.8,0.068938,-0.54279,0.83703,32.072 > view matrix models > #1,1,0,0,-6.7459,0,1,0,-9.7289,0,0,1,16.934,#2,-0.97764,0.13032,0.16502,54.467,-0.19865,-0.8297,-0.52167,116.17,0.068938,-0.54279,0.83703,30.336 > close session > open /Users/chiaramcallister/Downloads/1EEO.pdb 1EEO.pdb title: Crystal structure of protein tyrosine phosphatase 1B complexed with acetyl-E- L-E-F-ptyr-M-D-Y-E-NH2 [more info...] Chain information for 1EEO.pdb #1 --- Chain | Description | UniProt A | PTP1B | PTN1_HUMAN 1-321 B | acetyl-E-L-E-F-ptyr-M-D-Y-E-NH2 peptide | Non-standard residues in 1EEO.pdb #1 --- MG — magnesium ion NH2 — amino group > select /A 2648 atoms, 2481 bonds, 1 pseudobond, 519 residues, 2 models selected > select /B 87 atoms, 84 bonds, 14 residues, 1 model selected > hide atoms > show cartoons > color /A lightgray > show /B atoms > style /B stick Changed 87 atom styles > color /B & C orange > view matrix models #1,1,0,0,12.09,0,1,0,-6.8875,0,0,1,13.873 > select /B:PTR 16 atoms, 16 bonds, 1 residue, 1 model selected > show sel atoms > style sel ballstick Expected a keyword > color sel byelement > view sel > style sel ball Changed 16 atom styles > select zone /B:PTR 5 protein residues true Selected 142 atoms > show sel atoms > style sel stick Changed 142 atom styles > color sel byelement > select /B:PTR 16 atoms, 16 bonds, 1 residue, 1 model selected > hbonds sel restrict both reveal true 0 hydrogen bonds found > hbonds sel reveal true 14 hydrogen bonds found > view matrix models #1,1,0,0,11.6,0,1,0,-5.9816,0,0,1,14.389 > ~hbonds > hbonds /B:PTR restrict both reveal true 0 hydrogen bonds found > hbonds /B:PTR restrict both interModel false reveal true 0 hydrogen bonds found > hbonds sel reveal true 14 hydrogen bonds found > select solvent 226 atoms, 226 residues, 1 model selected > hide sel > cartoon suppressBackboneDisplay false > transparency #1 50 > cartoons Unknown command: cartoons > undo > redo > transparency #1 50cartoons Missing or invalid ""percent"" argument: Expected a number > transparency 50 cartoons > label /A:215,221 residues > view matrix models #1,1,0,0,9.2217,0,1,0,-4.7929,0,0,1,11.963 > clip slab true Expected a keyword > hide solvent > hide ligands Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select /B 87 atoms, 84 bonds, 5 pseudobonds, 14 residues, 2 models selected > hide sel > hide sel cartoons > show :PTR > select /A 2648 atoms, 2481 bonds, 1 pseudobond, 519 residues, 2 models selected > hide sel > hide sel cartoons > show :PTR zone 5 extend true Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > select zone /B:PTR 5 protein residues true Selected 142 atoms > show sel atoms > hide sel atoms > show sel cartoons > transparency 50 cartoons > transparency 70 cartoons > transparency 90 cartoons > transparency 50 cartoons > label /B:PTR 4 Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > label /B:PTR4 > hide all > show :PTR > show :PTR zone 4.5 extend true Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > cartoon suppressBackboneDisplay false > select PTR4 Expected an objects specifier or a keyword > select PTR 4 Expected an objects specifier or a keyword > show :PTR > select :PTR 16 atoms, 16 bonds, 1 residue, 1 model selected > select sel : show sel atoms > hide solvent > hide ~sel > select :PTR 16 atoms, 16 bonds, 1 residue, 1 model selected > select sel :> 3.5 & ~sel 2623 atoms, 2446 bonds, 1 pseudobond, 518 residues, 2 models selected > hide sel cartoons > hide sel atoms > view matrix models #1,1,0,0,14.4,0,1,0,-3.8904,0,0,1,15.436 > ui mousemode right select Drag select of 27 atoms, 4 residues, 26 bonds, 1 pseudobonds > select clear Drag select of 11 atoms, 3 residues, 11 bonds > select clear Drag select of 4 atoms, 1 residues, 4 bonds > hide sel > hide sel cartoons Drag select of 7 atoms, 1 residues, 6 bonds > hide sel atoms > hide sel cartoons > select clear Drag select of 4 atoms, 1 residues, 5 bonds > hide sel atoms Drag select of 1 atoms, 2 residues, 1 bonds Drag select of 2 residues, 1 bonds > select clear Drag select of 3 atoms, 4 bonds > hide sel atoms Drag select of 2 atoms, 2 residues, 3 bonds > select clear Drag select of 1 residues > hide sel atoms > select clear > view > label :PTR > show :48 > hide :48 > show :46 > color :PTR green > color :215,221,216 blue > undo > color :215,221,216 byhetero > color :215,221,216 & element C cornflower blue Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color :PTR byhetero > color :PTR & element C lime green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select /B:PTR 16 atoms, 16 bonds, 1 residue, 1 model selected > show sel atoms > style sel ballstick Expected a keyword > color sel & C orange > color sel byelement target a > view sel > select zone /B:PTR 4 protein residues true Selected 110 atoms > show sel atoms > style sel stick Changed 110 atom styles > color sel & C tan > color sel byelement target a > select clear > undo > color :PTR & element C orange Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color :PTR & element C #FF8C00 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color :PTR orange > color :PTR byelement > color :PTR & C orange > color :PTR & C lightorange Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color :PTR & C lyellow Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color :PTR & C yellow > color :PTR & C gray > select clear Drag select of 1 atoms, 1 bonds > select /A:262@OE1 1 atom, 1 residue, 1 model selected Drag select of 1 atoms, 3 bonds > show sel atoms > hide sel atoms > hide sel cartoons > undo Drag select of 7 atoms, 7 bonds > hide sel cartoons > hide sel atoms Drag select of 1 atoms > hide sel atoms ===== Log before crash end ===== Log: UCSF ChimeraX version: 1.12.dev202605010205 (2026-05-01) © 2016-2026 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 90.5 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.9 Locale: en_US.UTF-8 Qt version: PyQt6 6.10.2, Qt 6.10.0 Qt runtime version: 6.10.1 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: MGN93N/A Chip: Apple M1 Total Number of Cores: 8 (4 Performance and 4 Efficiency) Memory: 8 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: 3 dagen, 22 uur en 35 minuten Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Support: Metal 4 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: accessible-pygments: 0.0.5 aiohappyeyeballs: 2.6.1 aiohttp: 3.13.1 aiosignal: 1.4.0 alabaster: 1.0.0 annotated-types: 0.7.0 anyio: 4.13.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.1 attrs: 26.1.0 babel: 2.18.0 beautifulsoup4: 4.13.5 blockdiag: 3.0.0 blosc2: 4.1.2 bs4: 0.0.2 build: 1.3.0 certifi: 2025.7.14 cftime: 1.6.5 charset-normalizer: 3.4.7 ChimeraX-AddCharge: 1.5.20 ChimeraX-AddH: 2.2.8 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.6.2 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 3.2 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: 1.67.1 ChimeraX-AtomicLibrary: 14.4 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: 1.4.1 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.5 ChimeraX-ChemGroup: 2.0.2 ChimeraX-Clashes: 2.4 ChimeraX-Cluster: 1.0 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.8 ChimeraX-CommandLine: 1.3.1 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.12.dev202605010205 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: 1.2.1 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: 1.8.2 ChimeraX-Label: 1.4 ChimeraX-LightingGUI: 1.0 ChimeraX-ListInfo: 1.3.1 ChimeraX-Log: 1.2.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.3 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-MatchAlign: 1.1 ChimeraX-MatchMaker: 2.4 ChimeraX-MCopy: 1.0 ChimeraX-MCPServer: 0.2.0 ChimeraX-MDcrds: 2.19 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-Minimize: 1.3.8 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.16 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.23 ChimeraX-ModelPanel: 1.6.1 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: 1.15.4 ChimeraX-OpenFold: 1.0 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.13 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: 1.6 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.8.2 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: 3.5.12 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.18 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-SNFG: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.19.3 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: 2.5.3 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.4 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.50.6 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.2 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDock: 1.6.2 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: 8.3.3 colorama: 0.4.6 comm: 0.2.3 contourpy: 1.3.3 coverage: 7.13.5 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.2.4 debugpy: 1.8.20 decorator: 5.2.1 docutils: 0.21.2 executing: 2.2.1 filelock: 3.19.1 fonttools: 4.62.1 frozenlist: 1.8.0 funcparserlib: 2.0.0a0 glfw: 2.10.0 grako: 3.16.5 h11: 0.16.0 h5py: 3.16.0 html2text: 2025.4.15 httpcore: 1.0.9 httpx: 0.28.1 httpx-sse: 0.4.3 idna: 3.13 ihm: 2.2 imagecodecs: 2024.6.1 imagesize: 2.0.0 iniconfig: 2.3.0 ipykernel: 7.1.0 ipython: 9.9.0 ipython_pygments_lexers: 1.1.1 jedi: 0.19.2 Jinja2: 3.1.6 jsonschema: 4.26.0 jsonschema-specifications: 2025.9.1 jupyter_client: 8.8.0 jupyter_core: 5.9.1 kiwisolver: 1.5.0 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: 6.7.1 narwhals: 2.20.0 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: 8.4.0 openvr: 1.26.701 packaging: 25.0 ParmEd: 4.2.2 parso: 0.8.6 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: 4.9.6 plotly: 6.7.0 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: 2.13.3 pydantic-settings: 2.14.0 pydantic_core: 2.46.3 pydata-sphinx-theme: 0.17.1 pydicom: 2.4.4 Pygments: 2.18.0 pynmrstar: 3.5.1 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: 6.10.2 PyQt6-Qt6: 6.10.1 PyQt6-WebEngine-commercial: 6.10.0 PyQt6-WebEngine-Qt6: 6.10.1 PyQt6_sip: 13.10.3 pytest: 9.0.3 pytest-cov: 7.1.0 python-dateutil: 2.9.0.post0 python-dotenv: 1.2.2 python-multipart: 0.0.27 pyzmq: 27.1.0 qtconsole: 5.7.0 QtPy: 2.4.3 qtshim: 1.2.2 RandomWords: 0.4.0 referencing: 0.37.0 requests: 2.32.5 roman-numerals: 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: 9.0.4 sphinx-autodoc-typehints: 3.6.1 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: 3.4.1 stack-data: 0.6.3 starlette: 1.0.0 superqt: 0.7.6 tables: 3.10.2 tcia_utils: 3.2.1 tifffile: 2025.3.13 tinyarray: 1.2.5 tornado: 6.5.5 tqdm: 4.67.3 traitlets: 5.14.3 typing-inspection: 0.4.2 typing_extensions: 4.15.0 Unidecode: 1.4.0 urllib3: 2.6.3 uvicorn: 0.46.0 wcwidth: 0.6.0 webcolors: 24.11.1 wheel: 0.45.1 wheel-filename: 1.4.2 yarl: 1.23.0 }}} " defect assigned normal 1.12 Window Toolkit chimerax-programmers all ChimeraX