id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 16777 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x00000002a307f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a2073000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a1067000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002a005b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029f04f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029e043000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029d037000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029c02b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029b01f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029a013000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000299007000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001df079000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 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, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, PIL._imagingmath, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atom_search.ast, chimerax.chem_group._chem_group (total: 54) 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""factorPackIds"" : { }, ""deploymentId"" : 240000083 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | QCoreApplication::postEvent: Unexpected null receiver note | available bundle cache has not been initialized yet You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/esthernguyen/Downloads/8qfs.pdb format pdb No such file/path: /Users/esthernguyen/Downloads/8qfs.pdb > open /Users/esthernguyen/Downloads/8sv8.pdb format pdb No such file/path: /Users/esthernguyen/Downloads/8sv8.pdb > open PDB ID 4UN3 'PDB' has no suffix > open ID 4UN3 'ID' has no suffix > open 4un3 Summary of feedback from opening 4un3 fetched from pdb --- notes | Fetching compressed mmCIF 4un3 from http://files.rcsb.org/download/4un3.cif Fetching CCD MG from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/G/MG/MG.cif 4un3 title: Crystal structure of Cas9 bound to PAM-containing DNA target [more info...] Chain information for 4un3 #1 --- Chain | Description | UniProt A | SGRNA | B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368 C | TARGET DNA STRAND | D | NON-TARGET DNA STRAND | Non-standard residues in 4un3 #1 --- MG — magnesium ion > save Missing or invalid ""fileName"" argument: Expected a file name > save Missing or invalid ""fileName"" argument: Expected a file name > hide atoms > show atoms > hide atoms > hide cartoons > show cartoons > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > select solvent 405 atoms, 405 residues, 1 model selected > select solvent 405 atoms, 405 residues, 1 model selected > select H Nothing selected > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > select H Nothing selected > show target ab > hide target a > set bgColor white > hide target m > show target m > close > close # Expected a models specifier or a keyword > open 4un3 format mmcif fromDatabase pdb 4un3 title: Crystal structure of Cas9 bound to PAM-containing DNA target [more info...] Chain information for 4un3 #1 --- Chain | Description | UniProt A | SGRNA | B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368 C | TARGET DNA STRAND | D | NON-TARGET DNA STRAND | Non-standard residues in 4un3 #1 --- MG — magnesium ion > set bgColor black > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color plum > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > color red > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > select /B:1239 5 atoms, 4 bonds, 1 residue, 1 model selected > select /B:1240 6 atoms, 5 bonds, 1 residue, 1 model selected > select /B:1239 5 atoms, 4 bonds, 1 residue, 1 model selected Drag select of 2 residues > color sel pink > select clezr Expected an objects specifier or a keyword > select clear > center Unknown command: center > select clear > select all 13629 atoms, 13708 bonds, 140 pseudobonds, 1839 residues, 5 models selected > center sel Unknown command: center sel > center sel Unknown command: center sel > show solvent > delete solvent > hydrogen Unknown command: modelcif hydrogen > set bgColor white > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > ui tool show ""Show Sequence Viewer"" > color lightblue > select chain a Expected an objects specifier or a keyword > select /A 1736 atoms, 1942 bonds, 48 pseudobonds, 85 residues, 3 models selected > select /B 10694 atoms, 10877 bonds, 14 pseudobonds, 1310 residues, 3 models selected > color sel light blue > clear sel Unknown command: clear sel > clear Unknown command: clear > select clear > select /B 10694 atoms, 10877 bonds, 14 pseudobonds, 1310 residues, 3 models selected > color sel blue > color sel orange > delete sel Undo failed, probably because structures have been modified. > show /B > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > open new 'new' has no suffix > open 4un3 4un3 title: Crystal structure of Cas9 bound to PAM-containing DNA target [more info...] Chain information for 4un3 #2 --- Chain | Description | UniProt A | SGRNA | B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368 C | TARGET DNA STRAND | D | NON-TARGET DNA STRAND | Non-standard residues in 4un3 #2 --- MG — magnesium ion > close session > open 4un3 format mmcif fromDatabase pdb 4un3 title: Crystal structure of Cas9 bound to PAM-containing DNA target [more info...] Chain information for 4un3 #1 --- Chain | Description | UniProt A | SGRNA | B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368 C | TARGET DNA STRAND | D | NON-TARGET DNA STRAND | Non-standard residues in 4un3 #1 --- MG — magnesium ion > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > color sel orange > clear sel Unknown command: clear sel > select cler Expected an objects specifier or a keyword > select clear > hide cartoons > show cartoons > hide cartoons > show cartoons > select /A 1882 atoms, 1942 bonds, 58 pseudobonds, 231 residues, 3 models selected > color sel blue > clear sel Unknown command: clear sel > select clear > select /C 578 atoms, 634 bonds, 39 residues, 1 model selected > color sel pink > color sel darkred pink Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel hot pink > select clear > select /D 229 atoms, 255 bonds, 13 residues, 1 model selected > color sel green > select clear > hide /B > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > hide sel > hide sel cartoons > undo > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > color /B orange > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > select solvent 405 atoms, 405 residues, 1 model selected > select solvent 405 atoms, 405 residues, 1 model selected > delete sel > show atoms > hide atoms > show atoms > hide atoms > undo > select H Nothing selected > select solvent Nothing selected > select /D 227 atoms, 255 bonds, 11 residues, 1 model selected > select clear > select H Nothing selected > ui tool show ""Show Sequence Viewer"" > color /A pink > color /A steelblue > color /C yellow green > color / D red > ui tool show Distances Exactly two atoms must be selected! No distances to delete! > ui tool show ""Add Hydrogens"" > addh #!1 Summary of feedback from adding hydrogens to 4un3 #1 --- warnings | Not adding hydrogens to /A A 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /B LYS 797 CB because it is missing heavy-atom bond partners notes | Termini for 4un3 (#1) chain A determined from SEQRES records Termini for 4un3 (#1) chain B determined from SEQRES records Termini for 4un3 (#1) chain C determined from SEQRES records Termini for 4un3 (#1) chain D determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /B LYS 4, /B THR 386, /B SER 719, /B ASN 776, /B GLY 1030, /B LYS 1059, /B GLU 1253 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /B ASP 384, /B LYS 710, /B ARG 765, /B ASP 1012, /B ILE 1050, /B HIS 1241, /B GLN 1364 Chain-initial residues that are not actual 5' termini: /A A 1, /D DA 2 1358 hydrogen bonds Adding 'H' to /B LYS 4 Adding 'H' to /B THR 386 Adding 'H' to /B SER 719 Adding 'H' to /B ASN 776 Adding 'H' to /B GLY 1030 2 messages similar to the above omitted /B GLN 1364 is not terminus, removing H atom from 'C' /D DA 2 is not terminus, removing H atom from O5' 12183 hydrogens added > ui tool show Missing or invalid ""toolName"" argument: Expected a text string > ui tool show ""Show Sequence Viewer"" > ui tool show ""Add Hydrogens"" > addh #!1 Summary of feedback from adding hydrogens to 4un3 #1 --- warnings | Not adding hydrogens to /A A 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /B LYS 797 CB because it is missing heavy-atom bond partners notes | Termini for 4un3 (#1) chain A determined from SEQRES records Termini for 4un3 (#1) chain B determined from SEQRES records Termini for 4un3 (#1) chain C determined from SEQRES records Termini for 4un3 (#1) chain D determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /B LYS 4, /B THR 386, /B SER 719, /B ASN 776, /B GLY 1030, /B LYS 1059, /B GLU 1253 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /B ASP 384, /B LYS 710, /B ARG 765, /B ASP 1012, /B ILE 1050, /B HIS 1241, /B GLN 1364 Chain-initial residues that are not actual 5' termini: /A A 1, /D DA 2 1287 hydrogen bonds /B GLN 1364 is not terminus, removing H atom from 'C' /D DA 2 is not terminus, removing H atom from O5' 0 hydrogens added > ui tool show H-Bonds > hbonds sel reveal true Atom specifier selects no atoms > select /B 21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected > ui tool show H-Bonds > hbonds sel reveal true 1130 hydrogen bonds found > select clear > undo Undo failed, probably because structures have been modified. > hide atoms > undo > show atoms > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > delete all > open 4un3 format mmcif fromDatabase pdb 4un3 title: Crystal structure of Cas9 bound to PAM-containing DNA target [more info...] Chain information for 4un3 #1 --- Chain | Description | UniProt A | SGRNA | B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368 C | TARGET DNA STRAND | D | NON-TARGET DNA STRAND | Non-standard residues in 4un3 #1 --- MG — magnesium ion > select solvent 405 atoms, 405 residues, 1 model selected > delete sel Undo failed, probably because structures have been modified. > select all 13224 atoms, 13708 bonds, 125 pseudobonds, 1434 residues, 5 models selected > ui tool show ""Add Hydrogens"" > addh #!1 Summary of feedback from adding hydrogens to 4un3 #1 --- warnings | Not adding hydrogens to /A A 1 P because it is missing heavy-atom bond partners Not adding hydrogens to /B LYS 797 CB because it is missing heavy-atom bond partners notes | Termini for 4un3 (#1) chain A determined from SEQRES records Termini for 4un3 (#1) chain B determined from SEQRES records Termini for 4un3 (#1) chain C determined from SEQRES records Termini for 4un3 (#1) chain D determined from SEQRES records Chain-initial residues that are actual N termini: Chain-initial residues that are not actual N termini: /B LYS 4, /B THR 386, /B SER 719, /B ASN 776, /B GLY 1030, /B LYS 1059, /B GLU 1253 Chain-final residues that are actual C termini: Chain-final residues that are not actual C termini: /B ASP 384, /B LYS 710, /B ARG 765, /B ASP 1012, /B ILE 1050, /B HIS 1241, /B GLN 1364 Chain-initial residues that are not actual 5' termini: /A A 1, /D DA 2 1358 hydrogen bonds Adding 'H' to /B LYS 4 Adding 'H' to /B THR 386 Adding 'H' to /B SER 719 Adding 'H' to /B ASN 776 Adding 'H' to /B GLY 1030 2 messages similar to the above omitted /B GLN 1364 is not terminus, removing H atom from 'C' /D DA 2 is not terminus, removing H atom from O5' 12183 hydrogens added > select all H Expected a keyword > select clear > select hydrogen Expected an objects specifier or a keyword > select hydrogens Expected an objects specifier or a keyword > select H 12183 atoms, 1426 residues, 1 model selected > select clear > set bgColor black > set bgColor white > select /B 21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected > color /B dark green > select clear > color /A dark magenta > color /C orange > color /D deep pink > color /D deeppink blue Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color /D blue > color /D cadet blue > color /D dark blue > color /C cadet blue > hide /B > show/B Unknown command: show/B > show /B > hide /B > hide cartoons > show cartoons > hide cartoons > show cartoons > hide cartoons > show cartoons > select /B 21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected > hide sel > select /B 21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected > hide cartoons > show sel cartoons > select clear > show sel cartoons > select clear > cartoon > hide #!1 models > show #!1 models > select add #1 25407 atoms, 25891 bonds, 125 pseudobonds, 1434 residues, 5 models selected > select subtract #1 Nothing selected > select /B 21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected > hide sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > select /C:17 32 atoms, 34 bonds, 1 residue, 1 model selected > select /C:17-22 193 atoms, 208 bonds, 6 residues, 1 model selected > select /C:13 32 atoms, 33 bonds, 1 residue, 1 model selected > select /C:13-18 190 atoms, 204 bonds, 6 residues, 1 model selected > select /C:6 30 atoms, 31 bonds, 1 residue, 1 model selected > select /C:6-11 188 atoms, 200 bonds, 6 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > ui tool show ""Show Sequence Viewer"" > sequence chain /A Alignment identifier is 1/A > select /C:2 32 atoms, 34 bonds, 1 residue, 1 model selected > select /C:2-5 128 atoms, 138 bonds, 4 residues, 1 model selected > select /C:5 32 atoms, 34 bonds, 1 residue, 1 model selected > select /C:5-7 92 atoms, 98 bonds, 3 residues, 1 model selected > select /D:5 32 atoms, 33 bonds, 1 residue, 1 model selected > select /D:5-7 98 atoms, 105 bonds, 3 residues, 1 model selected > select /C:10 32 atoms, 33 bonds, 1 residue, 1 model selected > select /C:10-19 318 atoms, 341 bonds, 10 residues, 1 model selected > select /C:6 30 atoms, 31 bonds, 1 residue, 1 model selected > select /C:6-8 92 atoms, 98 bonds, 3 residues, 1 model selected > select /D:5 32 atoms, 33 bonds, 1 residue, 1 model selected > select /D:5-7 98 atoms, 105 bonds, 3 residues, 1 model selected > color sel red > name sel ""PAM"" ""sel"" is reserved and cannot be redefined > select /B 21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected > show /B > show sel cartoons > hide sel atoms > select clear > ui tool show Distances Exactly two atoms must be selected! > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select clear > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select subtract /D:6 Nothing selected Drag select of 3 residues Drag select of 2 residues > select /D:7 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:5 32 atoms, 33 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:7 33 atoms, 35 bonds, 1 residue, 1 model selected Drag select of 3 residues, 1 shapes > show sel target ab > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > style sel stick Changed 98 atom styles > style sel ball Changed 98 atom styles > style sel sphere Changed 98 atom styles > style sel stick Changed 98 atom styles > style sel ball Changed 98 atom styles > style sel ball Changed 98 atom styles > ui tool show Contacts > contacts sel ignoreHiddenModels true 161 contacts > undo > ui tool show Contacts > select clear Drag select of 19 pseudobonds > delete sel > hide sel Drag select of 16 pseudobonds > hide sel Drag select of 11 pseudobonds > hide sel > view clip false > select add #1.4 161 pseudobonds, 1 model selected > delete sel > hide sel > select subtract #1.4 Nothing selected > hide #1.4 models > show #1.4 models > hide #1.4 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > show #!1.3 models > hide #1.2 models > show #1.2 models > hide #1.2 models > show #1.2 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > hide #1.1 models > show #1.1 models > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:6 33 atoms, 35 bonds, 1 residue, 1 model selected > select /D:7 33 atoms, 35 bonds, 1 residue, 1 model selected Drag select of 3 residues > select /D:5 32 atoms, 33 bonds, 1 residue, 1 model selected > select add /D:6 65 atoms, 68 bonds, 2 residues, 1 model selected > select add /D:7 98 atoms, 103 bonds, 3 residues, 1 model selected > select /B 21560 atoms, 21743 bonds, 14 pseudobonds, 1310 residues, 3 models selected > select add /D:5 21592 atoms, 21776 bonds, 14 pseudobonds, 1311 residues, 3 models selected > select add /D:6 21625 atoms, 21811 bonds, 14 pseudobonds, 1312 residues, 3 models selected > select add /D:7 21658 atoms, 21846 bonds, 14 pseudobonds, 1313 residues, 3 models selected > ui tool show Contacts > contacts sel distanceOnly 4.0 ignoreHiddenModels true 93051 distances > select clear > show #1.4 models > hide #1.4 models > show #1.4 models > hide #1.4 models > select /B 21560 atoms, 21743 bonds, 86549 pseudobonds, 1310 residues, 4 models selected > hide #!1 models > show #!1 models > select add /D:5 21592 atoms, 21776 bonds, 86549 pseudobonds, 1311 residues, 4 models selected > select add /D:6 21625 atoms, 21811 bonds, 86549 pseudobonds, 1312 residues, 4 models selected > select add /D:7 21658 atoms, 21846 bonds, 86549 pseudobonds, 1313 residues, 4 models selected > ui tool show Distances > ui tool show Contacts > contacts sel restrict both distanceOnly 4.0 ignoreHiddenModels true 86965 distances > show #1.4 models > select add #1.4 21658 atoms, 21846 bonds, 86979 pseudobonds, 1313 residues, 4 models selected > select subtract #1.4 21658 atoms, 21846 bonds, 14 pseudobonds, 1313 residues, 3 models selected > select add #1.4 21658 atoms, 21846 bonds, 86979 pseudobonds, 1313 residues, 4 models selected > delete sel > undo Undo failed, probably because structures have been modified. > preset ""initial styles"" ""original look"" Using preset: Initial Styles / Original Look Preset implemented in Python; no expansion to individual ChimeraX commands available. > open 4un3 format mmcif fromDatabase pdb 4un3 title: Crystal structure of Cas9 bound to PAM-containing DNA target [more info...] Chain information for 4un3 #2 --- Chain | Description | UniProt A | SGRNA | B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368 C | TARGET DNA STRAND | D | NON-TARGET DNA STRAND | Non-standard residues in 4un3 #2 --- MG — magnesium ion > cloe Unknown command: cloe > cloeclose Unknown command: cloeclose > close > open 4un3 format mmcif fromDatabase pdb 4un3 title: Crystal structure of Cas9 bound to PAM-containing DNA target [more info...] Chain information for 4un3 #1 --- Chain | Description | UniProt A | SGRNA | B | CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1 | CAS9_STRP1 1-1368 C | TARGET DNA STRAND | D | NON-TARGET DNA STRAND | Non-standard residues in 4un3 #1 --- MG — magnesium ion > color /B slate blue > color/A red Unknown command: color/A red > color /A red > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color /A yellow green > color /B steel blue > color /C coral > color /D orange > color /D orangered > color /D tomato > color /D dark orange > color /C crimson > color /C tomato > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > hide sel > show sel > hide sel > hide sel cartoons > ui tool show ""Show Sequence Viewer"" > sequence chain /C Alignment identifier is 1/C > select /C:9 20 atoms, 21 bonds, 1 residue, 1 model selected > select /C:9-11 60 atoms, 65 bonds, 3 residues, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain /D Alignment identifier is 1/D > select /D:5 20 atoms, 21 bonds, 1 residue, 1 model selected > select /D:5-7 64 atoms, 71 bonds, 3 residues, 1 model selected > color sel red > color sel crimson > color sel teal > select clear > show cartoons > hide cartoons > show cartoons > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > hide sel cartoons > select /C:7-8 40 atoms, 44 bonds, 2 residues, 1 model selected > select /C:7-8 40 atoms, 44 bonds, 2 residues, 1 model selected > select /C:8-9 41 atoms, 45 bonds, 2 residues, 1 model selected > select /C:6-9 79 atoms, 87 bonds, 4 residues, 1 model selected > select /C:8 21 atoms, 23 bonds, 1 residue, 1 model selected > select /C:6-8 59 atoms, 65 bonds, 3 residues, 1 model selected > hide #1.1 models > show #1.1 models > hide #1.1 models > hide #1.2 models > hide #!1.3 models > show #!1.3 models > hide #!1.3 models > select add #1 13629 atoms, 13708 bonds, 140 pseudobonds, 1839 residues, 5 models selected > select subtract #1 Nothing selected > show cartoons > select /A 1882 atoms, 1942 bonds, 58 pseudobonds, 231 residues, 3 models selected > hide sel > hide sel cartoons > select /D 229 atoms, 255 bonds, 13 residues, 1 model selected > select /C 578 atoms, 634 bonds, 39 residues, 1 model selected > hide /C > hide sel cartoons > select add /D:2 596 atoms, 654 bonds, 40 residues, 1 model selected > select add /D:3 617 atoms, 677 bonds, 41 residues, 1 model selected Drag select of 1 residues, 2 shapes > select add /D:3 617 atoms, 677 bonds, 41 residues, 1 model selected > select add /D:4 638 atoms, 700 bonds, 42 residues, 1 model selected > hide sel cartoons > hide sel atoms > select add /D:12 660 atoms, 724 bonds, 43 residues, 1 model selected > select add /D:11 680 atoms, 745 bonds, 44 residues, 1 model selected > select add /D:9 701 atoms, 768 bonds, 45 residues, 1 model selected > select add /D:8 721 atoms, 789 bonds, 46 residues, 1 model selected > select add /D:10 741 atoms, 810 bonds, 47 residues, 1 model selected > hide sel cartoons > hide sel atoms > select add /D:7 763 atoms, 834 bonds, 48 residues, 1 model selected > select add /D:5 805 atoms, 855 bonds, 50 residues, 1 model selected > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > hide sel atoms > select subtract /D:7 783 atoms, 831 bonds, 49 residues, 1 model selected > select subtract /D:6 761 atoms, 831 bonds, 48 residues, 1 model selected > select subtract /D:5 741 atoms, 810 bonds, 47 residues, 1 model selected > select add /D:7 763 atoms, 834 bonds, 48 residues, 1 model selected > select add /D:6 785 atoms, 858 bonds, 49 residues, 1 model selected > select add /D:5 805 atoms, 879 bonds, 50 residues, 1 model selected > show sel cartoons > hide sel cartoons > show sel cartoons > hide sel atoms > show sel atoms > hide /C > hide sel cartoons > show sel atoms > show sel cartoons > select clear > select /D 229 atoms, 255 bonds, 13 residues, 1 model selected > select /C 578 atoms, 634 bonds, 39 residues, 1 model selected > hide sel > hide sel cartoons > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > hide sel cartoons > show sel atoms > hide sel atoms > show sel cartoons > select add /D:5 10960 atoms, 10898 bonds, 18 pseudobonds, 1557 residues, 3 models selected > select add /D:6 10982 atoms, 10922 bonds, 18 pseudobonds, 1558 residues, 3 models selected > select add /D:7 11004 atoms, 10946 bonds, 18 pseudobonds, 1559 residues, 3 models selected > label NGG Expected one of 'atoms', 'bonds', 'models', 'pseudobonds', or 'residues' or a keyword > select : in dna Expected an objects specifier or a keyword > select /C 578 atoms, 634 bonds, 39 residues, 1 model selected > select /D 229 atoms, 255 bonds, 13 residues, 1 model selected > select /D:5-7 64 atoms, 71 bonds, 3 residues, 1 model selected > label sel No distances to delete! > select /B & within 4 of /D:5-7 Expected a keyword > select /B within 4 of /D:5-7 Expected a keyword > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > select /B and /D:5-7 Expected a keyword > select /B & /D:5-7 Nothing selected > select /B & /D:5-7 Nothing selected > select /B, /D Expected an objects specifier or a keyword > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > select /B with /D Expected a keyword > select add /D:5 10960 atoms, 10898 bonds, 18 pseudobonds, 1557 residues, 3 models selected > select add /D:6 10982 atoms, 10922 bonds, 18 pseudobonds, 1558 residues, 3 models selected > select add /D:7 11004 atoms, 10946 bonds, 18 pseudobonds, 1559 residues, 3 models selected > select clear > select /B add /D:5-7 Expected a keyword > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > addcharge /D Using Amber 20 recommended default charges and atom types for standard residues 1 structure has non-integral total charge. Details in log. Here are the structures will non-integral total charge along with the particular residues from those structures with non-integral total charge: 4un3 #1: /D DA 2: -2.3889, /D DA 3: -2.7752, /D DA 4: -2.7752, /D DT 5: -2.5246, /D DG 6: -3.0838, /D DG 7: -3.0838, /D DT 8: -2.5246, /D DA 9: -2.7752, /D DT 10: -2.5246, /D DT 11: -2.5246, /D DG 12: -3.0838, /D HOH 2001: -0.834, and /D HOH 2002: -0.834 > select add /D 11169 atoms, 11132 bonds, 18 pseudobonds, 1569 residues, 3 models selected > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > select add /D:5-7 11004 atoms, 10948 bonds, 18 pseudobonds, 1559 residues, 3 models selected > ui tool show Distances > ui tool show Contacts > select :5-7 in DNA Expected a keyword > select :5-7 in /D Expected a keyword > select :5-7 209 atoms, 227 bonds, 6 pseudobonds, 12 residues, 2 models selected > select clear > select :5-7 209 atoms, 227 bonds, 6 pseudobonds, 12 residues, 2 models selected > select :5-7 209 atoms, 227 bonds, 6 pseudobonds, 12 residues, 2 models selected > select clear > select add /D:5 20 atoms, 21 bonds, 1 residue, 1 model selected > select add /D:6 42 atoms, 45 bonds, 2 residues, 1 model selected > select add /D:7 64 atoms, 69 bonds, 3 residues, 1 model selected > distance /D:5-7 in /B Expected a keyword > distance /D:5-7 Expected exactly two atoms and/or measurable objects (e.g. axes, planes), or one or more measurable objects and one or more atoms, got 64 atoms and 0 measurable objects > ui tool show Distances > distance style radius 4 > select zone Missing or invalid ""near"" argument: empty atom specifier > select #1.4 1 model selected > select subtract #1.4 Nothing selected > hide #1.4 models > show #1.4 models > select #1 13629 atoms, 13708 bonds, 140 pseudobonds, 1839 residues, 6 models selected > select clear > select /B,/D:5-7 Expected an objects specifier or a keyword > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > sel/B Unknown command: sel/B > select /B-D 11747 atoms, 11766 bonds, 37 pseudobonds, 1608 residues, 4 models selected > select /B /D:5-7 11004 atoms, 10948 bonds, 18 pseudobonds, 1559 residues, 3 models selected > select zone /B /D:5-7 cutoff 4 Missing or invalid ""range"" argument: Expected a number > select zone /B /D:5-7 4 Selected 673 atoms, 1 surfaces > label sel > center Unknown command: center > undo > show #1.4 models > hide #1.4 models > select add #1.4 1 model selected > show #1.4 models > delete sel > select delete Expected an objects specifier or a keyword > select subtract #1.4 Nothing selected > hide #1.4 models > show #1.4 models > hide #1.4 models > show #1.4 models > hide #1.4 models > delete #1.4 > ui tool show Contacts > show atoms > sel/A /C Unknown command: sel/A /C > select /A /C 2460 atoms, 2576 bonds, 101 pseudobonds, 270 residues, 3 models selected > hide sel atoms > select /D 229 atoms, 255 bonds, 13 residues, 1 model selected > show sel atoms > hide sel cartoons > show sel cartoons > hide sel cartoons > select solvent 405 atoms, 405 residues, 1 model selected > hide solvent > select /D:6@O5' 1 atom, 1 residue, 1 model selected > select /D:7@P 1 atom, 1 residue, 1 model selected > style sel sphere Changed 0 atom styles > select /D 229 atoms, 255 bonds, 13 residues, 1 model selected > style sel ball Changed 229 atom styles > style sel sphere Changed 229 atom styles > style sel stick Changed 229 atom styles > style sel ball Changed 229 atom styles > lighting soft > lighting simple > select clear > view > view center Expected an objects specifier or a view name or a keyword > view > label #!1 attribute name > transparency #!1 60 > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > transparency (#!1 & sel) 70 > select clear > cartoon hide #!1 > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected No Surface models open > select > ::name=""ALA""::name=""ARG""::name=""ASN""::name=""ASP""::name=""CYS""::name=""GLN""::name=""GLU""::name=""GLY""::name=""HIS""::name=""ILE""::name=""LEU""::name=""LYS""::name=""MET""::name=""PHE""::name=""PRO""::name=""SER""::name=""THR""::name=""TRP""::name=""TYR""::name=""VAL"" 10690 atoms, 10877 bonds, 6 pseudobonds, 1306 residues, 2 models selected > ui tool show ""Color Actions"" > color sel bynucleotide > color sel byhetero > color sel byelement > color sel bynucleotide > color sel bychain > color sel bypolymer > color sel bychain > color sel bynucleotide > color sel byelement > color sel byhetero > color sel bynucleotide > color sel hot pink > color sel cornflower blue > color sel light gray > color sel gray > color sel dark gray > color sel gray > color sel light gray > color sel dim gray > color sel dark gray > color sel gray > color sel purple > color sel light gray > color sel gray > color sel bynucleotide Alignment identifier is 1/B Destroying pre-existing alignment with identifier 1/B Alignment identifier is 1/B > show sel surfaces > color sel tan > color list No custom colors. 248 builtin colors: alice blue , aliceblue , antique white , antiquewhite , aqua , aquamarine , azure , beige , bisque , black , blanched almond , blanchedalmond , blue , blue violet , blueviolet , brown , burly wood , burlywood , cadet blue , cadetblue , chartreuse , chocolate , coral , cornflower blue , cornflowerblue , cornsilk , crimson , cyan , dark blue , dark cyan , dark goldenrod , dark gray , dark green , dark grey , dark khaki , dark magenta , dark olive green , dark orange , dark orchid , dark red , dark salmon , dark sea green , dark seagreen , dark slate blue , dark slate gray , dark slate grey , dark turquoise , dark violet , darkblue , darkcyan , darkgoldenrod , darkgray , darkgreen , darkgrey , darkkhaki , darkmagenta , darkolivegreen , darkorange , darkorchid , darkred , darksalmon , darkseagreen , darkslateblue , darkslategray , darkslategrey , darkturquoise , darkviolet , deep pink , deep sky blue , deep skyblue , deeppink , deepskyblue , dim gray , dim grey , dimgray , dimgrey , dodger blue , dodgerblue , fire brick , firebrick , floral white , floralwhite , forest green , forestgreen , fuchsia , gainsboro , ghost white , ghostwhite , gold , goldenrod , gray , green , green yellow , greenyellow , grey , honeydew , hot pink , hotpink , indian red , indianred , indigo , ivory , khaki , lavender , lavender blush , lavenderblush , lawn green , lawngreen , lemon chiffon , lemonchiffon , light blue , light coral , light cyan , light goldenrod yellow , light gray , light green , light grey , light pink , light salmon , light sea green , light seagreen , light sky blue , light skyblue , light slate gray , light slate grey , light steel blue , light yellow , lightblue , lightcoral , lightcyan , lightgoldenrodyellow , lightgray , lightgreen , lightgrey , lightpink , lightsalmon , lightseagreen , lightskyblue , lightslategray , lightslategrey , lightsteelblue , lightyellow , lime , lime green , limegreen , linen , magenta , maroon , medium aquamarine , medium blue , medium orchid , medium purple , medium sea green , medium seagreen , medium slate blue , medium spring green , medium turquoise , medium violet red , mediumaquamarine , mediumblue , mediumorchid , mediumpurple , mediumseagreen , mediumslateblue , mediumspringgreen , mediumturquoise , mediumvioletred , midnight blue , midnightblue , mint cream , mintcream , misty rose , mistyrose , moccasin , navajo white , navajowhite , navy , old lace , oldlace , olive , olive drab , olivedrab , orange , orange red , orangered , orchid , pale goldenrod , pale green , pale turquoise , pale violet red , palegoldenrod , palegreen , paleturquoise , palevioletred , papaya whip , papayawhip , peach puff , peachpuff , peru , pink , plum , powder blue , powderblue , purple , rebecca purple , rebeccapurple , red , rosy brown , rosybrown , royal blue , royalblue , saddle brown , saddlebrown , salmon , sandy brown , sandybrown , sea green , seagreen , seashell , sienna , silver , sky blue , skyblue , slate blue , slate gray , slate grey , slateblue , slategray , slategrey , snow , spring green , springgreen , steel blue , steelblue , tan , teal , thistle , tomato , transparent , turquoise , violet , wheat , white , white smoke , whitesmoke , yellow , yellow green , and yellowgreen . > color sel peachpuff > color sel palegreen goldrenrod Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color sel pale goldenrod > color sel lace Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel old lace > color sel tan > ui tool show ""Side View"" > lighting flat > lighting full > lighting soft > lighting simple > lighting soft > lighting full > lighting simple > lighting full > select clear > transparency #1.5#!1 40 > transparency #1.5#!1 30 > surface style solid > transparency #1.5#!1 0 > transparency #1.5#!1 10 > transparency #1.5#!1 0 > volume hide No volumes specified > nucleotides atoms > style nucleic stick Changed 2526 atom styles > nucleotides fill > style nucleic stick Changed 2526 atom styles > nucleotides slab > style nucleic stick Changed 2526 atom styles > nucleotides tube/slab shape box > nucleotides tube/slab shape ellipsoid > nucleotides tube/slab shape muffler > nucleotides ladder > nucleotides stubs > nucleotides ladder > nucleotides atoms > style nucleic stick Changed 2526 atom styles > nucleotides fill > style nucleic stick Changed 2526 atom styles > nucleotides ladder > hide surfaces > show cartoons > hide cartoons > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > show sel cartoons > hide sel atoms > show sel atoms > hide sel atoms > show sel atoms > hide solvents Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models', 'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword > hide solvent > select clear > select /B 10940 atoms, 10877 bonds, 18 pseudobonds, 1556 residues, 3 models selected > show sel cartoons > hide sel atoms > select /D:5-7 64 atoms, 71 bonds, 3 residues, 1 model selected > show sel cartoons > select /D 229 atoms, 255 bonds, 13 residues, 1 model selected > show sel cartoons > select clear > ui tool show Contacts > help help:user/tools/clashes.html > select sel : select /B /D:5-7 11004 atoms, 10948 bonds, 18 pseudobonds, 1559 residues, 3 models selected > select /D:5-7 64 atoms, 71 bonds, 3 residues, 1 model selected > select sel : label sel > show #1.4 models > hide #1.4 models > show #1.4 models > hide #1.4 models > hide #1.5 models > show #1.5 models > hide #1.5 models > show #1.5 models > show #1.4 models > hide #1.4 models > hide #1.5 models > show #1.5 models > color sel pink > color sel teal > select clear > select add /B:1136 6 atoms, 5 bonds, 1 residue, 1 model selected Drag select of 4 residues > select /B:1174 11 atoms, 11 bonds, 1 residue, 1 model selected > select add /B:1137 18 atoms, 18 bonds, 2 residues, 2 models selected > select subtract /B:1174 7 atoms, 7 bonds, 1 residue, 2 models selected > select add /B:1107 16 atoms, 15 bonds, 2 residues, 2 models selected > select add /B:1136 22 atoms, 20 bonds, 3 residues, 2 models selected > select add /B:1139 29 atoms, 26 bonds, 4 residues, 2 models selected > select add /B:1200 38 atoms, 34 bonds, 5 residues, 2 models selected > select add /B:1216 44 atoms, 39 bonds, 6 residues, 2 models selected > select add /B:1215 49 atoms, 43 bonds, 7 residues, 2 models selected > select add /B:1219 58 atoms, 51 bonds, 8 residues, 2 models selected > select add /B:1221 67 atoms, 59 bonds, 9 residues, 2 models selected > select add /B:1320 72 atoms, 63 bonds, 10 residues, 2 models selected > select add /B:1335 83 atoms, 73 bonds, 11 residues, 2 models selected > select add /B:1333 94 atoms, 83 bonds, 12 residues, 2 models selected ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro17,1 Model Number: MYDC2LL/A Chip: Apple M1 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.61.4 OS Loader Version: 10151.61.4 Software: System Software Overview: System Version: macOS 14.2.1 (23C71) Kernel Version: Darwin 23.2.0 Time since boot: 62 days, 7 hours, 9 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 8 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal LG HDR 4K: Resolution: 3840 x 2160 (2160p/4K UHD 1 - Ultra High Definition) UI Looks like: 1920 x 1080 @ 30.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX