id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14892 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.0-x86_64-i386-64bit ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x000000032521e000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032421b000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000323218000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000322215000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000321212000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032020f000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031f20c000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031e209000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031d206000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031c203000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031b200000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031a1fd000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003191fa000 (most recent call first): File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x0000000205093240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 157 in asArray File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 146 in File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/OpenGL/arrays/lists.py"", line 145 in asArray File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 2828 in set_matrix File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 817 in set_projection_matrix File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 725 in _use_shader File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 801 in _opengl_shader File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/opengl.py"", line 698 in shader File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 818 in _draw_geometry File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 787 in draw_self File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 780 in draw File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1567 in _draw_multiple File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/drawing.py"", line 1554 in draw_opaque File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 258 in _draw_scene File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/graphics/view.py"", line 188 in draw File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 84 in draw_new_frame File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/updateloop.py"", line 150 in _redraw_timer_callback File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: 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.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, 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, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, 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, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, numpy.linalg.lapack_lite, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 62) {""app_name"":""ChimeraX"",""timestamp"":""2024-04-03 08:59:38.00 -0500"",""app_version"":""1.7.0"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.0.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.0 (23A344)"",""roots_installed"":0,""name"":""ChimeraX"",""incident_id"":""40AB6C73-0735-44B8-A987-A804CF0B51E3""} { ""uptime"" : 140000, ""procRole"" : ""Foreground"", ""version"" : 2, ""userID"" : 501, ""deployVersion"" : 210, ""modelCode"" : ""MacBookPro18,3"", ""coalitionID"" : 26441, ""osVersion"" : { ""train"" : ""macOS 14.0"", ""build"" : ""23A344"", ""releaseType"" : ""User"" }, ""captureTime"" : ""2024-04-03 08:58:04.5071 -0500"", ""codeSigningMonitor"" : 1, ""incident"" : ""40AB6C73-0735-44B8-A987-A804CF0B51E3"", ""pid"" : 60030, ""translated"" : true, ""cpuType"" : ""X86-64"", ""roots_installed"" : 0, ""bug_type"" : ""309"", ""procLaunch"" : ""2024-04-01 15:26:50.7089 -0500"", ""procStartAbsTime"" : 1803712739761, ""procExitAbsTime"" : 3510229654792, ""procName"" : ""ChimeraX"", ""procPath"" : ""\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX"", ""bundleInfo"" : {""CFBundleShortVersionString"":""1.7.0"",""CFBundleVersion"":""1.7.0.0"",""CFBundleIdentifier"":""edu.ucsf.cgl.ChimeraX""}, ""storeInfo"" : {""deviceIdentifierForVendor"":""E7645B00-7015-5C35-8B97-5BFF52D821FD"",""thirdParty"":true}, ""parentProc"" : ""launchd"", ""parentPid"" : 1, ""coalitionName"" : ""edu.ucsf.cgl.ChimeraX"", ""crashReporterKey"" : ""F5D56411-1169-49D5-5797-B94C04536BCA"", ""codeSigningID"" : ""edu.ucsf.cgl.ChimeraX"", ""codeSigningTeamID"" : ""LWV8X224YF"", ""codeSigningFlags"" : 570491649, ""codeSigningValidationCategory"" : 6, ""codeSigningTrustLevel"" : 4294967295, ""wakeTime"" : 2176, ""sleepWakeUUID"" : ""474FEBFB-BE5D-4ED0-B20A-BA8BB61AC3B3"", ""sip"" : ""enabled"", ""vmRegionInfo"" : ""0xa9 is not in any region. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/jonathanmartin/Downloads/AF-Q825Z7-F1-model_v4.pdb AF-Q825Z7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for lysine--TRNA ligase (Q825Z7) [more info...] Chain information for AF-Q825Z7-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | lysine--TRNA ligase | Q825Z7_STRAW 1-1093 > select /A:249:548 23 atoms, 22 bonds, 2 residues, 1 model selected > select /A:2490548 Nothing selected > select /A:249-548 2339 atoms, 2390 bonds, 300 residues, 1 model selected > select ~sel & ##selected 6057 atoms, 6192 bonds, 793 residues, 1 model selected > color sel seafoam Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel seafoam green Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel green > 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 olivedrab > lighting flat > set bgColor white > lighting simple > lighting soft > lighting full > lighting flat > ui mousemode right select > select clear > open /Users/jonathanmartin/code/mprf_figures/fullmprf.cxs opened ChimeraX session > open /Users/jonathanmartin/Downloads/AF-Q825Z7-F1-model_v4.pdb AF-Q825Z7-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for lysine--TRNA ligase (Q825Z7) [more info...] Chain information for AF-Q825Z7-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | lysine--TRNA ligase | Q825Z7_STRAW 1-1093 > ui tool show ""Modeller Comparative"" > ui tool show Matchmaker > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7duw.pdb, chain A (#1) with AF-Q825Z7-F1-model_v4.pdb, chain A (#2), sequence alignment score = 677.4 RMSD between 132 pruned atom pairs is 1.288 angstroms; (across all 503 pairs: 24.592) > select clear > ui mousemode right translate > select /B:249-548 2156 atoms, 2205 bonds, 2 pseudobonds, 283 residues, 2 models selected > select /A:249-548 4495 atoms, 4595 bonds, 2 pseudobonds, 583 residues, 3 models selected > ui tool show Matchmaker > matchmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7duw.pdb, chain A (#1) with AF-Q825Z7-F1-model_v4.pdb, chain A (#2), sequence alignment score = 677.4 RMSD between 132 pruned atom pairs is 1.288 angstroms; (across all 503 pairs: 24.592) > matchmaker #2 & sel to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7duw.pdb, chain A (#1) with AF-Q825Z7-F1-model_v4.pdb, chain A (#2), sequence alignment score = 474 RMSD between 131 pruned atom pairs is 1.170 angstroms; (across all 292 pairs: 4.377) > matchmaker #2 to #1 & sel Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker 7duw.pdb, chain A (#1) with AF-Q825Z7-F1-model_v4.pdb, chain A (#2), sequence alignment score = 209.4 RMSD between 18 pruned atom pairs is 1.402 angstroms; (across all 198 pairs: 12.849) > ui mousemode right ""translate selected models"" > view matrix models > #1,1,0,0,14.656,0,1,0,-1.6416,0,0,1,-2.3523,#2,-0.008061,-0.749,-0.66252,135.31,-0.65721,0.50332,-0.56103,129.34,0.75367,0.43089,-0.49631,124.07 > view matrix models > #1,1,0,0,-14.026,0,1,0,1.415,0,0,1,0.22615,#2,-0.008061,-0.749,-0.66252,106.63,-0.65721,0.50332,-0.56103,132.39,0.75367,0.43089,-0.49631,126.64 > view matrix models > #1,1,0,0,-0.75215,0,1,0,0.062859,0,0,1,-0.15683,#2,-0.008061,-0.749,-0.66252,119.9,-0.65721,0.50332,-0.56103,131.04,0.75367,0.43089,-0.49631,126.26 > ui mousemode right ""translate selected models"" > ui mousemode right select > select clear > select add #2 8396 atoms, 8582 bonds, 1093 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.008061,-0.749,-0.66252,195.64,-0.65721,0.50332,-0.56103,123.03,0.75367,0.43089,-0.49631,120.21 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.40268,-0.44748,-0.7985,192.87,-0.49401,0.62816,-0.60114,122.13,0.77059,0.63653,0.031887,127.85 > view matrix models > #2,0.096323,-0.98146,0.16569,209.78,0.91194,0.02031,-0.40983,129.12,0.39887,0.19058,0.89699,142.78 > close session > open /Users/jonathanmartin/Downloads/AF-O69916-F1-model_v4.pdb AF-O69916-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for putative integral membrane lysyl-TRNA synthetase (O69916) [more info...] Chain information for AF-O69916-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | putative integral membrane lysyl-TRNA synthetase | O69916_STRCO 1-589 > select /A:250-547 2397 atoms, 2454 bonds, 298 residues, 1 model selected > select ~sel & ##selected 2293 atoms, 2353 bonds, 291 residues, 1 model selected > color sel olivedrab > ui mousemode right select > select clear > undo > select /A:250-600 2733 atoms, 2798 bonds, 340 residues, 1 model selected > select ~sel & ##selected 1957 atoms, 2009 bonds, 249 residues, 1 model selected > select up 1958 atoms, 2009 bonds, 250 residues, 1 model selected > select up 1968 atoms, 2019 bonds, 250 residues, 1 model selected > color sel olivedrab > select clear > undo > redo > undo > redo > color sel olivedrab > select clear Drag select of 11 residues > ui mousemode right ""translate selected models"" > ui mousemode right select > ui mousemode right translate > ui mousemode right select > select clear > ui mousemode right translate > close session > open /Users/jonathanmartin/Downloads/1a01.pdb 1a01.pdb title: Hemoglobin (val Β1 met, TRP Β37 ala) mutant [more info...] Chain information for 1a01.pdb #1 --- Chain | Description | UniProt A C | hemoglobin (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (β chain) | HBB_HUMAN 2-146 Non-standard residues in 1a01.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) > open /Users/jonathanmartin/Downloads/AF-P04078-F1-model_v4.pdb AF-P04078-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for glutamine synthetase cytosolic isozyme (P04078) [more info...] Chain information for AF-P04078-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | glutamine synthetase cytosolic isozyme | GLNA1_MEDSA 1-356 > close session > open /Users/jonathanmartin/Downloads/AF-P04078-F1-model_v4.pdb AF-P04078-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for glutamine synthetase cytosolic isozyme (P04078) [more info...] Chain information for AF-P04078-F1-model_v4.pdb #1 --- Chain | Description | UniProt A | glutamine synthetase cytosolic isozyme | GLNA1_MEDSA 1-356 > select /A:151-254 780 atoms, 803 bonds, 104 residues, 1 model selected > color sel tomato > lighting soft > select 2762 atoms, 2837 bonds, 356 residues, 1 model selected > ui mousemode right select > select clear > open /Users/jonathanmartin/Downloads/AF-P04771-F1-model_v4.pdb AF-P04771-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for glutamine synthetase Pr-2 (P04771) [more info...] Chain information for AF-P04771-F1-model_v4.pdb #2 --- Chain | Description | UniProt A | glutamine synthetase Pr-2 | GLNA2_PHAVU 1-356 > select add #2 2769 atoms, 2845 bonds, 356 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #2,1,0,0,-29.088,0,1,0,18.961,0,0,1,40.47 > ui mousemode right translate > select #2/A:1-356 2769 atoms, 2845 bonds, 356 residues, 1 model selected > select /A 5531 atoms, 5682 bonds, 712 residues, 2 models selected > select /A1 Nothing selected > select /1 Nothing selected > select /#2 Expected an objects specifier or a keyword > select /A#2 5531 atoms, 5682 bonds, 712 residues, 2 models selected > select #2 2769 atoms, 2845 bonds, 356 residues, 1 model selected > select #2:164-347 1424 atoms, 1456 bonds, 184 residues, 1 model selected > color sel olivedrab > ui mousemode right select > select clear > select #1 2762 atoms, 2837 bonds, 356 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.75335,-0.6371,0.16299,1.9557,0.35283,0.18243,-0.91773,2.4313,0.55495,0.74888,0.36222,-2.3299 > view matrix models > #1,0.71594,-0.62008,0.32083,2.3394,0.34448,-0.085953,-0.93485,3.611,0.60726,0.77982,0.15207,-3.0863 > ui mousemode right select > select clear > select #1 2762 atoms, 2837 bonds, 356 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,0.60695,-0.76715,0.20757,1.631,-0.18272,-0.38889,-0.90298,0.99208,0.77345,0.51014,-0.37621,-2.983 > ui mousemode right select > select clear > select #1 2762 atoms, 2837 bonds, 356 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #1,-0.61072,0.58022,0.53886,-13.312,0.48226,0.81228,-0.32807,3.2399,-0.62805,0.059512,-0.77589,-14.072 > view matrix models > #1,-0.61803,0.60119,0.50658,-13.633,0.509,0.79707,-0.32495,3.5475,-0.59913,0.057018,-0.79862,-13.936 > view matrix models > #1,-0.67063,0.60563,-0.42833,-18.652,-0.5727,-0.78971,-0.21992,3.1554,-0.47145,0.097818,0.87645,-4.9141 > view matrix models > #1,-0.11492,-0.4338,-0.89365,-11.263,0.61598,-0.73689,0.27849,14.974,-0.77933,-0.51847,0.3519,-6.9196 > view matrix models > #1,0.042998,-0.50957,-0.85936,-9.4379,0.6923,-0.60497,0.39336,15.5,-0.72033,-0.61185,0.32676,-6.1006 > ui mousemode right select > select clear > select #1 2762 atoms, 2837 bonds, 356 residues, 1 model selected > select clear > select #1 2762 atoms, 2837 bonds, 356 residues, 1 model selected Drag select of 4 residues > select #1 2762 atoms, 2837 bonds, 356 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #1,0.042998,-0.50957,-0.85936,-8.3937,0.6923,-0.60497,0.39336,3.5469,-0.72033,-0.61185,0.32676,-7.6078 > ui mousemode right select > select clear > ui mousemode right translate > color #1 olivedrab > color #2 tomato > select #1:106-356 1957 atoms, 2012 bonds, 251 residues, 1 model selected > color sel tan > select #2:103-356 1983 atoms, 2040 bonds, 254 residues, 1 model selected > color sel tan > ui mousemode right select > select clear > open /Users/jonathanmartin/Downloads/P04771.fa Summary of feedback from opening /Users/jonathanmartin/Downloads/P04771.fa --- notes | Alignment identifier is P04771.fa Associated AF-P04771-F1-model_v4.pdb chain A to P04771 1-356 with 0 mismatches Opened 1 sequences from P04771.fa > open /Users/jonathanmartin/Downloads/AF-P38094-F1-model_v4.pdb AF-P38094-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for protein flug (P38094) [more info...] Chain information for AF-P38094-F1-model_v4.pdb #3 --- Chain | Description | UniProt A | protein flug | FLUG_EMENI 1-865 > select #3 6808 atoms, 6964 bonds, 865 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-8.5042,0,1,0,8.6919,0,0,1,14.886 > view matrix models #3,1,0,0,-31.618,0,1,0,70.496,0,0,1,77.299 > select #3:540-865 2538 atoms, 2597 bonds, 326 residues, 1 model selected > select #3:540-865 2538 atoms, 2597 bonds, 326 residues, 1 model selected > color sel tan > view matrix models #3,1,0,0,-31.557,0,1,0,70.549,0,0,1,77.282 > ui mousemode right select > select #3/A:840 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > ui mousemode right translate > select #3 6808 atoms, 6964 bonds, 865 residues, 1 model selected > ui mousemode right ""rotate selected models"" > ui mousemode right ""translate selected models"" > view matrix models #3,1,0,0,-59.876,0,1,0,62.086,0,0,1,82.026 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.94483,-0.25099,-0.21049,-57.833,0.22636,0.96474,-0.13434,62.549,0.23678,0.079283,0.96832,81.546 > view matrix models > #3,-0.36897,-0.88309,0.28985,-56.815,0.27874,0.19236,0.9409,57.296,-0.88666,0.42796,0.17517,88.228 > view matrix models > #3,-0.53216,-0.54558,0.64742,-59.538,0.38946,0.52124,0.75936,57.475,-0.75175,0.65625,-0.064898,88.962 > view matrix models > #3,-0.34396,-0.55936,0.75419,-60.592,0.51221,0.5614,0.64998,57.826,-0.78697,0.60987,0.093415,88.126 > ui mousemode right ""translate selected models"" > view matrix models > #3,-0.34396,-0.55936,0.75419,-29.283,0.51221,0.5614,0.64998,64.042,-0.78697,0.60987,0.093415,87.213 > view matrix models > #3,-0.34396,-0.55936,0.75419,-28.401,0.51221,0.5614,0.64998,64.468,-0.78697,0.60987,0.093415,87.415 > view matrix models > #3,-0.34396,-0.55936,0.75419,-27.658,0.51221,0.5614,0.64998,68.664,-0.78697,0.60987,0.093415,85.388 > ui mousemode right select Drag select of 1 residues > select clear > select #3 6808 atoms, 6964 bonds, 865 residues, 1 model selected > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.74679,-0.65488,-0.11588,-24.164,0.30283,0.17971,0.93595,68.143,-0.59211,-0.73405,0.33252,86.511 > view matrix models > #3,0.6004,0.77247,-0.20692,-26.531,0.56706,-0.22879,0.79126,69.446,0.56388,-0.59241,-0.5754,89.568 > ui mousemode right ""translate selected models"" > view matrix models > #3,0.6004,0.77247,-0.20692,-60.443,0.56706,-0.22879,0.79126,84.09,0.56388,-0.59241,-0.5754,63.161 > ui mousemode right translate > ui mousemode right ""translate selected models"" > view matrix models > #3,0.6004,0.77247,-0.20692,-50.161,0.56706,-0.22879,0.79126,69.568,0.56388,-0.59241,-0.5754,54.328 > ui mousemode right ""rotate selected models"" > view matrix models > #3,0.58861,0.74608,-0.3113,-49.406,0.52286,-0.057652,0.85047,68.89,0.61657,-0.66336,-0.42403,53.406 > view matrix models > #3,0.60186,0.77392,-0.19701,-50.232,0.57067,-0.24421,0.78403,69.642,0.55866,-0.58431,-0.58863,54.405 > view matrix models > #3,0.68915,0.71427,-0.12204,-50.762,0.6097,-0.48055,0.63035,71.087,0.39159,-0.50881,-0.76666,55.731 > view matrix models > #3,0.62945,0.69811,-0.34124,-49.19,0.73922,-0.40263,0.53986,71.216,0.23949,-0.59206,-0.76948,56.262 > view matrix models > #3,0.76622,0.60702,-0.2108,-50.11,0.64255,-0.7267,0.24295,74.069,-0.0057148,-0.32161,-0.94686,57.303 > view matrix models > #3,0.81102,0.55706,-0.17868,-50.297,0.57986,-0.80592,0.11941,75.177,-0.077481,-0.20045,-0.97664,57.37 > view matrix models > #3,0.83388,0.52676,-0.16482,-50.365,0.54045,-0.83988,0.050089,75.784,-0.11205,-0.13085,-0.98505,57.338 > view matrix models > #3,0.88663,0.44027,-0.14159,-50.429,0.42396,-0.89608,-0.1315,77.326,-0.18477,0.056567,-0.98115,57.039 > view matrix models > #3,0.77568,0.59741,-0.20352,-50.155,0.63076,-0.7447,0.21808,74.295,-0.021276,-0.29754,-0.95447,57.33 > ui mousemode right select > select clear > ui tool show Matchmaker > matchmaker #3 to #2 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-P04771-F1-model_v4.pdb, chain A (#2) with AF-P38094-F1-model_v4.pdb, chain A (#3), sequence alignment score = 336.2 RMSD between 116 pruned atom pairs is 1.034 angstroms; (across all 325 pairs: 7.930) > select #3 6808 atoms, 6964 bonds, 865 residues, 1 model selected > ui mousemode right ""translate selected models"" > view matrix models > #3,0.73034,-0.14093,-0.66838,-65.677,0.45373,-0.63135,0.62891,57.235,-0.51062,-0.76258,-0.39716,86.07 > ui mousemode right select > select clear > undo > ui mousemode right ""translate selected models"" > view matrix models > #3,0.73034,-0.14093,-0.66838,-69.499,0.45373,-0.63135,0.62891,62.81,-0.51062,-0.76258,-0.39716,93.721 > ui mousemode right select > select clear > hide #2 models > show #2 models > hide #2 models > hide #3 models > ui mousemode right translate > hide #1 models > show #2 models > hide #2 models > show #3 models > show #2 models > show #1 models > save /Users/jonathanmartin/Downloads/test.cxs > ui tool show Matchmaker > matchmaker #2-3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-P04078-F1-model_v4.pdb, chain A (#1) with AF-P04771-F1-model_v4.pdb, chain A (#2), sequence alignment score = 1774.1 RMSD between 355 pruned atom pairs is 0.145 angstroms; (across all 356 pairs: 0.297) Matchmaker AF-P04078-F1-model_v4.pdb, chain A (#1) with AF-P38094-F1-model_v4.pdb, chain A (#3), sequence alignment score = 314.9 RMSD between 117 pruned atom pairs is 1.048 angstroms; (across all 328 pairs: 8.385) > hide #2 models > show #2 models > ui tool show Matchmaker > ui tool show ""Modeller Comparative"" > hide #1 models > hide #2 models > show #2 models > show #1 models > ui mousemode right select Drag select of 1074 residues > select subtract #3/A:1 8380 atoms, 1073 residues, 3 models selected > ui tool show ""Show Sequence Viewer"" > sequence chain #3/A Alignment identifier is 3/A > save /Users/jonathanmartin/Downloads/flug_selection.fasta format fasta > alignment 3/A > select clear > close session > open /Users/jonathanmartin/Downloads/1a01.pdb format pdb 1a01.pdb title: Hemoglobin (val Β1 met, TRP Β37 ala) mutant [more info...] Chain information for 1a01.pdb #1 --- Chain | Description | UniProt A C | hemoglobin (α chain) | HBA_HUMAN 1-141 B D | hemoglobin (β chain) | HBB_HUMAN 2-146 Non-standard residues in 1a01.pdb #1 --- HEM — protoporphyrin IX containing Fe (HEME) > select 4738 atoms, 4664 bonds, 20 pseudobonds, 776 residues, 2 models selected > hide sel atoms > select clear > select /B,D 2410 atoms, 2378 bonds, 10 pseudobonds, 388 residues, 2 models selected > hide sel atoms > hide sel cartoons > select /A 1160 atoms, 1143 bonds, 5 pseudobonds, 190 residues, 2 models selected > hide sel cartoons Drag select of 11 residues > select clear > ui mousemode right translate > color aqua green Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > color /A green > color /B green > color /C green > lighting flat > lighting soft > lighting flat > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting flat > color /C olive > color /C gray > select ~sel & ##selected Nothing selected > color /C maroon > 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 /C orchid > color /C medium purple > color /C slate blue > color /C violet > color /C blue violet > color /C darkred > select /B 1208 atoms, 1189 bonds, 5 pseudobonds, 197 residues, 2 models selected > show sel atoms > hide sel atoms > show sel cartoons > select /C 1168 atoms, 1143 bonds, 5 pseudobonds, 198 residues, 2 models selected > hide sel cartoons > color /B cobalt Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color /B dodger blue > close session > open /Users/jonathanmartin/Downloads/test.cxs format session opened ChimeraX session > ui tool show Matchmaker > matchmaker #2-3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker AF-P04078-F1-model_v4.pdb, chain A (#1) with AF-P04771-F1-model_v4.pdb, chain A (#2), sequence alignment score = 1774.1 RMSD between 355 pruned atom pairs is 0.145 angstroms; (across all 356 pairs: 0.297) Matchmaker AF-P04078-F1-model_v4.pdb, chain A (#1) with AF-P38094-F1-model_v4.pdb, chain A (#3), sequence alignment score = 314.9 RMSD between 117 pruned atom pairs is 1.048 angstroms; (across all 328 pairs: 8.385) ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7 (2023-12-19) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 86 OpenGL renderer: Apple M1 Pro OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,3 Model Number: MKGT3LL/A Chip: Unknown Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 16 GB System Firmware Version: 10151.1.1 OS Loader Version: 10151.1.1 Software: System Software Overview: System Version: macOS 14.0 (23A344) Kernel Version: Darwin 23.0.0 Time since boot: 3 days, 22 hours, 59 minutes Graphics/Displays: Apple M1 Pro: Chipset Model: Apple M1 Pro Type: GPU Bus: Built-In Total Number of Cores: 16 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3024 x 1964 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.13 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.1 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.3 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.13 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.3 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.3 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.2 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.0 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.0 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.5.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.3 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.5.8 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 Pillow: 10.0.1 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.7 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.5 sphinxcontrib-htmlhelp: 2.0.4 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.6 sphinxcontrib-serializinghtml: 1.1.9 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.3 urllib3: 2.1.0 wcwidth: 0.2.12 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX