id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 14898 Crash deleting hydrogens sindelar@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.2.1-arm64-arm-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Calculated structure H bonds Deleted hydrogens Fatal Python error: Segmentation fault Thread 0x00000003730db000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029e73f000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029d733000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029c727000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029b71b000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000029a70f000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000299703000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002986f7000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002976eb000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002966df000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002956d3000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000002946c7000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028d793000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000028c787000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001dbfd1000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 811 in delete File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/delete.py"", line 50 in delete_atoms File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/delete.py"", line 33 in delete File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2908 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: 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, 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Bytes before following region: 4335157248\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 102654000-102658000 [ 16K] r-x\/r-x SM=COW ...acOS\/ChimeraX"", ""exception"" : {""codes"":""0x0000000000000001, 0x0000000000000000"",""rawCodes"":[1,0],""type"":""EXC_BAD_ACCESS"",""signal"":""SIGSEGV"",""subtype"":""KERN_INVALID_ADDRESS at 0x0000000000000000""}, ""termination"" : {""flags"":0,""code"":11,""namespace"":""SIGNAL"",""indicator"":""Segmentation fault: 11"",""byProc"":""ChimeraX"",""byPid"":62225}, ""vmregioninfo"" : ""0 is not in any region. 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""SIRI_TEXT_TO_SPEECH"" : ""65f35e7e74b6f500a45abe2d"" }, ""deploymentId"" : 240000429 } ], ""experiments"" : [ ] } } ===== Log before crash start ===== Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open > /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/fig4a_new_fignumber.cxs Opened myo1c_adp_a_best.pdb map 20 as #2300.6, grid size 88,87,81, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_b_best.pdb map 20 as #2301.6, grid size 88,87,81, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_a_best.pdb map 20 as #2302.6, grid size 78,75,77, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_b_best.pdb map 20 as #2303.6, grid size 78,75,77, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_a_best.pdb map 20 as #2304.6, grid size 76,77,81, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_b_best.pdb map 20 as #2305.6, grid size 77,77,81, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_a_best.pdb map 20 as #2306.6, grid size 84,71,73, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_b_best.pdb map 20 as #2307.6, grid size 84,72,71, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_a_best.pdb map 20 as #2308.6, grid size 68,67,68, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_b_best.pdb map 20 as #2309.6, grid size 68,67,69, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_a_best.pdb map 20 as #2310.6, grid size 101,93,117, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_adp_b_best.pdb map 20 as #2311.6, grid size 101,93,118, pixel 2, shown at level 0.01, step 1, values float32 opened ChimeraX session > open > /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/fig3f.cxs Opened myo1c_rigor_best_win.mrc as #3, grid size 224,224,224, pixel 1.33, shown at step 1, values float32 Opened copy of myo1c_adp_a_best.pdb map 10 as #24, grid size 45,39,54, pixel 3.33, shown at step 1, values float32 Opened myo1c_adp_a_best.mrc as #1, grid size 224,224,224, pixel 1.35, shown at step 1, values float32 Opened myo1c_adp_b_best.mrc as #2, grid size 224,224,224, pixel 1.35, shown at step 1, values float32 Opened myo1c_adp_a_best.pdb map 4 as #301, grid size 51,44,52, pixel 1.33, shown at step 1, values float32 Opened myo1c_delntr_rigor_best.mrc as #4, grid size 224,224,224, pixel 1.34, shown at step 1, values float32 opened ChimeraX session > open > /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/myo1c_subdomain_transforms_rigor_to_delntr_ploop.cxs Opened myo1c_rigor_best.pdb map 20 as #2300.6, grid size 89,86,81, pixel 2, shown at step 1, values float32 Opened myo1c_delntr_rigor_best.pdb map 20 as #2301.6, grid size 88,86,81, pixel 2, shown at step 1, values float32 Opened myo1c_rigor_best.pdb map 20 as #2302.6, grid size 78,75,77, pixel 2, shown at step 1, values float32 Opened myo1c_delntr_rigor_best.pdb map 20 as #2303.6, grid size 78,75,77, pixel 2, shown at step 1, values float32 Opened myo1c_rigor_best.pdb map 20 as #2304.6, grid size 77,77,81, pixel 2, shown at step 1, values float32 Opened myo1c_delntr_rigor_best.pdb map 20 as #2305.6, grid size 77,77,81, pixel 2, shown at step 1, values float32 Opened myo1c_rigor_best.pdb map 20 as #2306.6, grid size 84,72,71, pixel 2, shown at step 1, values float32 Opened myo1c_delntr_rigor_best.pdb map 20 as #2307.6, grid size 85,71,72, pixel 2, shown at step 1, values float32 Opened myo1c_rigor_best.pdb map 20 as #2308.6, grid size 68,67,69, pixel 2, shown at step 1, values float32 Opened myo1c_delntr_rigor_best.pdb map 20 as #2309.6, grid size 68,67,69, pixel 2, shown at step 1, values float32 Opened myo1c_rigor_best.pdb map 20 as #2310.6, grid size 102,93,117, pixel 2, shown at step 1, values float32 Opened myo1c_delntr_rigor_best.pdb map 20 as #2311.6, grid size 102,94,118, pixel 2, shown at step 1, values float32 Opened myo1c_rigor_refine3.pdb map 20 as #2312.6, grid size 88,86,81, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2313.6, grid size 88,86,81, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_rigor_refine3.pdb map 20 as #2314.6, grid size 78,75,77, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2315.6, grid size 78,75,77, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_rigor_refine3.pdb map 20 as #2316.6, grid size 77,77,81, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2317.6, grid size 76,77,81, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_rigor_refine3.pdb map 20 as #2318.6, grid size 84,72,71, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2319.6, grid size 84,71,72, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_rigor_refine3.pdb map 20 as #2320.6, grid size 68,67,69, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2321.6, grid size 68,67,69, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_rigor_refine3.pdb map 20 as #2322.6, grid size 101,93,117, pixel 2, shown at level 0.01, step 1, values float32 Opened myo1c_delntr_rigor_refine4.pdb map 20 as #2323.6, grid size 102,94,117, pixel 2, shown at level 0.01, step 1, values float32 opened ChimeraX session > style sphere Changed 156083 atom styles > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > show #!5 models > hide #!1 models > hide #!5 models > select #3/P:158 12 atoms, 11 bonds, 1 residue, 1 model selected > select #3/P:157 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel atoms > hide H > hide #!3 models > show #!3 models > select #3/P:108@CA 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > show sel atoms > hide H > show #!1 models > hide #!3 models > style #!1 stick Changed 31301 atom styles > style #!1 sphere Changed 31301 atom styles > show #!3 models > select #1/P:53,107-108,157 46 atoms, 43 bonds, 4 residues, 1 model selected > hide sel atoms > hide #!1 models > open > /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_vols/myo1c_adp_b_best.pdb Chain information for myo1c_adp_b_best.pdb #7 --- Chain | Description B C D | No description available P | No description available R | No description available > select #7 31465 atoms, 31792 bonds, 1988 residues, 1 model selected > hide sel atoms > show sel cartoons > matchmaker #7 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_b_best.pdb, chain P (#7), sequence alignment score = 548.4 RMSD between 106 pruned atom pairs is 0.333 angstroms; (across all 106 pairs: 0.333) > hide #!3 models > show #!1 models > show #!2 models > hide #!2 models > color #7 lightgray atoms > color #7/P:143-387,529-566 gold atoms > color #7/P:388-442,437-528,565-584 chocolate atoms > color #7/P:627-900 pink atoms > color #7/P:1-126,584-626 lightblue atoms > color #7/P:127-142 50,100,50 atoms > color #7/R pink atoms > color #7/P:1-11 magenta atoms > transparency #7 30 atoms > color #7 lightgray ribbons > color #1/P:MG 0,0,75 ribbons > color #7/P:143-387,529-566 gold ribbons > color #7/P:388-442,437-528,565-584 chocolate ribbons > color #7/P:627-900 pink ribbons > color #7/P:1-126,584-626 lightblue ribbons > color #7/P:127-142 50,100,50 ribbons > color #7/R pink ribbons > color #7/P:1-11 magenta ribbons > transparency #7 30 ribbons > color #7 byhetero > ribbon #7 > ribbon #7,1,3,2 > hide #!1 models > select clear > graphics silhouettes true width 1 > graphics silhouettes true width 2 > view name t23 > zoom 0.3 moved plane near -200.64222072851862 [-0.46188862 0.72357466 0.51293139] moved plane far -200.64222072851862 [-0.46188862 0.72357466 0.51293139] > color #7 lightgray atoms > color #7/P:127-387,529-566 gold atoms > color #7/P:388-442,437-528,565-584 chocolate atoms > color #7/P:627-900 pink atoms > color #7/P:1-126,584-626 lightblue atoms > color #7/R pink atoms > color #7/P:1-11 magenta atoms > transparency #7 30 atoms > color #7 lightgray ribbons > color #1/P:MG 0,0,75 ribbons > color #7/P:127-387,529-566 gold ribbons > color #7/P:388-442,437-528,565-584 chocolate ribbons > color #7/P:627-900 pink ribbons > color #7/P:1-126,584-626 lightblue ribbons > color #7/R pink ribbons > color #7/P:1-11 magenta ribbons > transparency #7 30 ribbons > color #7 byhetero > view t23 > select #7/P:53,107-108,157 46 atoms, 43 bonds, 4 residues, 1 model selected > show sel atoms > hide H > graphics silhouettes true width 3 > ~ribbon se > cartoon hide se Expected an atoms specifier or a keyword > ~ribbon sel > style sel stick Changed 46 atom styles > style sel sphere Changed 46 atom styles > select clear > ~show #1-10 m > show #1 models > select #1/P:53,107-108,157 46 atoms, 43 bonds, 4 residues, 1 model selected > ~ribbon sel > style sphere sel Expected a keyword > ~ribbon sel > style sel sphere Changed 46 atom styles > show sel atoms > ~ribbon sel > style sel sphere Changed 46 atom styles > show sel atoms > hide H > show #!2 models > select clear > hide #!2 models > show #!2 models > hide #!2 models > show #7 models > transparency #7 30 ribbons > transparency #7 30 atoms > hide #!1 models > show #!1 models > transparency #1 0 atoms > transparency #1 0 ribbons > transparency #7 30 ribbons > transparency #7 70 ribbons > transparency #7 70 atoms > transparency #7 100 atoms > transparency #7 70 atoms > transparency #7 90 atoms > transparency #7 90 ribbons > ~show #1-10 m > show #1,7 models > ~show #1-10 m > show #3,7 models > transparency #3 0 ribbons > transparency #3 0 atoms > ~show #1 > ~show #1-10 m > show #1,3 models > transparency #1 90 atoms > transparency #1 90 ribbons > transparency #1 0 atoms > matchmaker #3 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_a_best.pdb, chain P (#3), sequence alignment score = 543.6 RMSD between 106 pruned atom pairs is 0.472 angstroms; (across all 106 pairs: 0.472) > matchmaker #7 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_b_best.pdb, chain P (#7), sequence alignment score = 548.4 RMSD between 106 pruned atom pairs is 0.333 angstroms; (across all 106 pairs: 0.333) > clip front off > clip back off > ribbon #1 > select #3/P:53,107-108,157 46 atoms, 43 bonds, 1 pseudobond, 4 residues, 2 models selected > ~ribbon sel > show sel > hide H > ~show #1-10 m > show #1,7 models > transparency #7 0 atoms > transparency #7 0 ribbons > ~show #1-10 m > show #3,7 models > ~show #3 > transparency #3 90 atoms > transparency #3 90 ribbons > ~show #1-10 m > show #1,7 models > ~show #1-10 m > show #1,3 models > ~show #1-10 m > show #3 models > combine #3 > ribbon #3 > ~show #1-10 m > show #3 models > ~show #1-10 m > show #8 models > transparency #8 0 ribbons > select #8/P:53,107-108,157 46 atoms, 43 bonds, 4 residues, 1 model selected > show sel&~H > transparency #8 0 atoms > style sel stick Changed 46 atom styles > clip near -1\ Invalid ""near"" argument: Expected 'off' or a number > clip near -1 > select #8/P:109@N 1 atom, 1 residue, 1 model selected > show sel > ui tool show ""Selection Inspector"" > setattr sel r ribbon_hide_backbone false Assigning ribbon_hide_backbone attribute to 1 item > style sel stick Changed 1 atom style > select #8/P:106@C 1 atom, 1 residue, 1 model selected > show sel atoms > style sel stick Changed 1 atom style > ui tool show ""Selection Inspector"" > setattr sel r ribbon_hide_backbone false Assigning ribbon_hide_backbone attribute to 1 item > hide sel atoms > select #8/P:54@N 1 atom, 1 residue, 1 model selected > show sel atoms > ui tool show ""Selection Inspector"" > setattr sel r ribbon_hide_backbone false Assigning ribbon_hide_backbone attribute to 1 item > style sel stick Changed 1 atom style > clip near -1 > clip near 1 > select #8/P:110 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 50 atoms, 49 bonds, 5 residues, 1 model selected > select up 52 atoms, 50 bonds, 6 residues, 1 model selected > select up 64 atoms, 62 bonds, 6 residues, 1 model selected > setattr sel r ribbon_hide_backbone true Assigning ribbon_hide_backbone attribute to 6 items > setattr sel r ribbon_hide_backbone false Assigning ribbon_hide_backbone attribute to 6 items > show sel cartoons > select #8/P:107 11 atoms, 10 bonds, 1 residue, 1 model selected > setattr sel r ribbon_hide_backbone true Assigning ribbon_hide_backbone attribute to 1 item > setattr sel r ribbon_hide_backbone false Assigning ribbon_hide_backbone attribute to 1 item > hide sel cartoons > select #8/P:108 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel cartoons > view t23 > clip near -1 > clip near 1 > select clear > view t23 > clip near -1 > select #8/P:243 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 160 atoms, 159 bonds, 11 residues, 1 model selected > select up 11612 atoms, 11736 bonds, 711 residues, 1 model selected > select down 160 atoms, 159 bonds, 11 residues, 1 model selected > hide sel cartoons > select #8/P:245 12 atoms, 11 bonds, 1 residue, 1 model selected > select up 238 atoms, 239 bonds, 14 residues, 1 model selected > hide sel cartoons > color #7 lightgray atoms > color #7/P:127-387,529-566 gold atoms > color #7/P:388-442,437-528,565-584 chocolate atoms > color #7/P:627-900 pink atoms > color #7/P:1-126,584-626 lightblue atoms > color #7/R pink atoms > color #7/P:1-11 magenta atoms > transparency #7 30 atoms > color #7 lightgray ribbons > color #1/P:MG 0,0,75 ribbons > color #7/P:127-387,529-566 gold ribbons > color #7/P:388-442,437-528,565-584 chocolate ribbons > color #7/P:627-900 pink ribbons > color #7/P:1-126,584-626 lightblue ribbons > color #7/R pink ribbons > color #7/P:1-11 magenta ribbons > transparency #7 30 ribbons > color #7 byhetero > color #8 lightgray atoms > color #8/P:127-387,529-566 gold atoms > color #8/P:388-442,437-528,565-584 chocolate atoms > color #8/P:627-900 pink atoms > color #8/P:1-126,584-626 lightblue atoms > color #8/R pink atoms > color #8/P:1-11 magenta atoms > transparency #8 30 atoms > color #8 lightgray ribbons > color #1/P:MG 0,0,75 ribbons > color #8/P:127-387,529-566 gold ribbons > color #8/P:388-442,437-528,565-584 chocolate ribbons > color #8/P:627-900 pink ribbons > color #8/P:1-126,584-626 lightblue ribbons > color #8/R pink ribbons > color #8/P:1-11 magenta ribbons > transparency #8 30 ribbons > color #8 byhetero > select #8/P:593 14 atoms, 14 bonds, 1 residue, 1 model selected > select add #8/P:592 36 atoms, 35 bonds, 2 residues, 1 model selected > select add #8/P:607 55 atoms, 53 bonds, 3 residues, 1 model selected > select down 55 atoms, 53 bonds, 3 residues, 1 model selected > select up 374 atoms, 378 bonds, 22 residues, 1 model selected > hide sel cartoons > select #8/P:43 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #8/P:37 38 atoms, 36 bonds, 2 residues, 1 model selected > select up 134 atoms, 135 bonds, 7 residues, 1 model selected > select up 11612 atoms, 11736 bonds, 711 residues, 1 model selected > select down 134 atoms, 135 bonds, 7 residues, 1 model selected > select add #8/P:33 158 atoms, 158 bonds, 8 residues, 1 model selected > select up 328 atoms, 330 bonds, 18 residues, 1 model selected > hide sel cartoons Drag select of 5 residues > select up 146 atoms, 144 bonds, 9 residues, 1 model selected > hide sel cartoons Drag select of 5 residues > hide sel cartoons > clip far -1 > clip far 1 > select #8/P:83 10 atoms, 9 bonds, 1 residue, 1 model selected Drag select of 4 residues > select add #8/P:76 98 atoms, 23 bonds, 6 residues, 1 model selected Drag select of 2 residues Drag select of 4 residues > select up 775 atoms, 781 bonds, 47 residues, 1 model selected > hide sel cartoons > clip far 1 Drag select of 11 residues > select up 221 atoms, 222 bonds, 15 residues, 1 model selected > hide sel cartoons Drag select of 6 residues > select up 566 atoms, 573 bonds, 34 residues, 1 model selected Drag select of 3 residues Drag select of 8 residues Drag select of 1 residues Drag select of 2 residues Drag select of 5 residues > select up 535 atoms, 542 bonds, 32 residues, 1 model selected > hide sel cartoons > show sel cartoons > select #8/P:400 17 atoms, 16 bonds, 1 residue, 1 model selected > select up 358 atoms, 361 bonds, 21 residues, 1 model selected > select add #8/P:397 369 atoms, 371 bonds, 22 residues, 1 model selected > select add #8/P:396 383 atoms, 384 bonds, 23 residues, 1 model selected > hide sel cartoons Drag select of 7 residues > select up 229 atoms, 232 bonds, 14 residues, 1 model selected > hide sel cartoons > select #8/P:184 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #8/P:355 31 atoms, 30 bonds, 2 residues, 1 model selected > select add #8/P:202 51 atoms, 50 bonds, 3 residues, 1 model selected > select up 724 atoms, 731 bonds, 45 residues, 1 model selected > select add #8/P:188 739 atoms, 745 bonds, 46 residues, 1 model selected > select add #8/P:191 763 atoms, 768 bonds, 47 residues, 1 model selected > select up 871 atoms, 880 bonds, 53 residues, 1 model selected > hide sel cartoons Drag select of 18 residues > select up 876 atoms, 877 bonds, 53 residues, 1 model selected > hide sel cartoons > select #8/P:363 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 49 atoms, 48 bonds, 3 residues, 1 model selected > hide sel cartoons > select #8/P:65 17 atoms, 17 bonds, 1 residue, 1 model selected > select up 135 atoms, 136 bonds, 7 residues, 1 model selected > hide sel cartoons Drag select of 4 residues > select up 207 atoms, 208 bonds, 13 residues, 1 model selected > hide sel cartoons Drag select of 1 residues > select up 65 atoms, 65 bonds, 4 residues, 1 model selected > select add #8/P:366 84 atoms, 83 bonds, 5 residues, 1 model selected > select up 279 atoms, 281 bonds, 18 residues, 1 model selected > hide sel cartoons > select #8/P:390 20 atoms, 20 bonds, 1 residue, 1 model selected > select up 177 atoms, 180 bonds, 11 residues, 1 model selected > hide sel cartoons > select #8/P:48,62,131-180,101-126,380-386,587-591 1375 atoms, 1379 bonds, 90 residues, 1 model selected > select #8/P:48-62,131-180,101-126,380-386,587-591 1598 atoms, 1606 bonds, 103 residues, 1 model selected > view t23 > clip far -1 > clip far 1 > ~ribbon #8 > ribbon sel > clip far 1 > ~ribbon #1-10 > select #1-8/P:48-62,131-180,101-126,380-386,587-591 11186 atoms, 11242 bonds, 2 pseudobonds, 721 residues, 8 models selected > ribbon sel > ~show #1-10 m > show #1,3 models > transparency #1 0 ribbons > select clear > select #2-8/P:53,107-108,157 276 atoms, 258 bonds, 2 pseudobonds, 24 residues, 7 models selected > show sel&~H > transparency sel 0 > transparency sel 0 atoms > ~ribbon sel > ~show #1-10 m > show #8 models > ~show #1-10 m > show #1,3 models > ~show #1-10 m > show #8 models > ~show #1-10 m > show #1,3 models > color #1-8 lightgray atoms > color #1-8/P:127-387,529-566 gold atoms > color #1-8/P:388-442,437-528,565-584 chocolate atoms > color #1-8/P:627-900 pink atoms > color #1-8/P:1-126,584-626 lightblue atoms > color #1-8/R pink atoms > color #1-8/P:1-11 magenta atoms > transparency #1-8 30 atoms > color #1-8 lightgray ribbons > color #1-8/P:127-387,529-566 gold ribbons > color #1-8/P:388-442,437-528,565-584 chocolate ribbons > color #1-8/P:627-900 pink ribbons > color #1-8/P:1-126,584-626 lightblue ribbons > color #1-8/R pink ribbons > color #1-8/P:1-11 magenta ribbons > transparency #1-8 30 ribbons > color #1-8 byhetero > transparency #1 90 ribbons > hide #!3 models > show #!3 models > transparency #3 0 ribbons > transparency #2-10 0 > transparency #2-10 0 atoms > ~show #1-10 m > show #8 models > ~show #1-10 m > show #1,3 models > hide #!3 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > hide #!1 models > show #!3 models > show #!8 models > matchmaker #7 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_b_best.pdb, chain P (#7), sequence alignment score = 548.4 RMSD between 106 pruned atom pairs is 0.333 angstroms; (across all 106 pairs: 0.333) > matchmaker #2 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_delntr_rigor_best.pdb, chain P (#2), sequence alignment score = 556.2 RMSD between 106 pruned atom pairs is 0.197 angstroms; (across all 106 pairs: 0.197) > matchmaker #3 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_a_best.pdb, chain P (#3), sequence alignment score = 543.6 RMSD between 106 pruned atom pairs is 0.472 angstroms; (across all 106 pairs: 0.472) > matchmaker #4 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_rigor_best.pdb, chain P (#4), sequence alignment score = 559.2 RMSD between 106 pruned atom pairs is 0.156 angstroms; (across all 106 pairs: 0.156) > matchmaker #5 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_delntr_rigor_best.pdb, chain P (#5), sequence alignment score = 556.2 RMSD between 106 pruned atom pairs is 0.195 angstroms; (across all 106 pairs: 0.195) > matchmaker #7 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with myo1c_adp_b_best.pdb, chain P (#7), sequence alignment score = 548.4 RMSD between 106 pruned atom pairs is 0.333 angstroms; (across all 106 pairs: 0.333) > matchmaker #8 to #1/P:388-409,442-525@ca,n,c,o 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 myo1c_rigor_best.pdb, chain P (#1) with copy of myo1c_adp_a_best.pdb, chain P (#8), sequence alignment score = 543.6 RMSD between 106 pruned atom pairs is 0.472 angstroms; (across all 106 pairs: 0.472) > ~show #1-10 m > show #8 models > ~show #1-10 m > show #1,3 models > style sphere Changed 218715 atom styles > select clear > ~show #1-10 m > show #8 models > style sphere Changed 218715 atom styles > ~show #1-10 m > show #1,3 models > hide #!1 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > hide #!8 models > show #!8 models > select #8 31167 atoms, 31490 bonds, 2 pseudobonds, 1968 residues, 2 models selected > ui tool show ""Selection Inspector"" > setattr sel r ribbon_hide_backbone true Assigning ribbon_hide_backbone attribute to 1968 items > transparency #1-10 0 atoms > transparency #1-10 0 ribbons > transparency #8 90 ribbons > transparency #8 0 atoms > ~show #1-10 m > show #1,10 models > ~show #1-10 m > show #1,8 models > ~show #8 > select #1-7/P:53,107-108,157 276 atoms, 258 bonds, 2 pseudobonds, 24 residues, 7 models selected > show sel > hide H > ~ribbon sel > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #7,8 models > select ~sel & ##selected 187200 atoms, 189160 bonds, 6 pseudobonds, 11822 residues, 11 models selected > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #1,8 models > ~show #1-10 m > show #3,8 models > select clear > ~show #1-10 m > show #7,8 models > style #7#!8 stick Changed 62632 atom styles > ~show #1-10 m > show #3,8 models > style #!3,8 stick Changed 62334 atom styles > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > style #!5,8 sphere Changed 62288 atom styles > ~show #1-10 m > show #3,8 models > style #!3,8 sphere Changed 62334 atom styles > select #3/P:53@CG 1 atom, 1 residue, 1 model selected > select add #3/P:157@OD1 2 atoms, 2 residues, 1 model selected > select up 28 atoms, 26 bonds, 2 residues, 1 model selected > style sel ball Changed 28 atom styles > select clear > style #!3,8 ball Changed 62334 atom styles > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #5,8 models > style #!5,8 ball Changed 62288 atom styles > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > hide #7 models > show #7 models > hide #!8 models > show #!8 models > hide #!8 models > select #7/P:592 22 atoms, 21 bonds, 1 residue, 1 model selected > show sel cartoons > select up 188 atoms, 190 bonds, 12 residues, 1 model selected > show sel cartoons > select #7/P:604 15 atoms, 14 bonds, 1 residue, 1 model selected > show sel cartoons > select up 186 atoms, 187 bonds, 10 residues, 1 model selected > show sel cartoons > select #7/P:592-604 203 atoms, 205 bonds, 13 residues, 1 model selected > select up 374 atoms, 378 bonds, 22 residues, 1 model selected > hide sel cartoons > save > /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/fig3d_p_loop.cxs > show #!1 models > style sel stick Changed 374 atom styles > select clear > style #7#!1 stick Changed 62766 atom styles > hide #!1 models > select #7/P:53@CA 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel cartoons > style sel sphere Changed 14 atom styles > style sel ball Changed 14 atom styles > select clear > select #7/P:108@O 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #7/P:107@C 8 atoms, 6 bonds, 2 residues, 1 model selected > select up 18 atoms, 17 bonds, 2 residues, 1 model selected > style sel sphere Changed 18 atom styles > select #7/P:157@CA 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > style sel ball Changed 14 atom styles > show sel cartoons > save > /Users/charless/Documents/documents_icloud/workworkwork_icloud/manuscripts_icloud/2023_shashank_myo1c_icloud/data_structures_icloud/final_figures/fig3d_p_loop.cxs > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > style stick Changed 218715 atom styles > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #5,8 models > ~show #1-10 m > show #3,8 models > ~show #1-10 m > show #7,8 models > select #8/P:48-62,131-180,101-126,380-386,587-591 1598 atoms, 1606 bonds, 103 residues, 1 model selected > show sel cartoons > select clear > select #8/P:53,107-108,157 46 atoms, 43 bonds, 4 residues, 1 model selected > hide sel cartoons > show sel atoms > hide H > transparency sel 90 a Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency sel 90 atoms > hide sel cartoons > show sel atoms > select up 438 atoms, 439 bonds, 29 residues, 1 model selected > select down 46 atoms, 43 bonds, 4 residues, 1 model selected > hide H > select #8/P:53,107-108,157 46 atoms, 43 bonds, 4 residues, 1 model selected > ~show #1-10 m > show #3,8 models > select clear > ~show #1-10 m > show #7,8 models > ~show #1-10 m > show #7,8 models > select #8/P:53,107-108,157 46 atoms, 43 bonds, 4 residues, 1 model selected > hide sel atoms > show sel cartoons > select #7/P:53,107-108,157 46 atoms, 43 bonds, 4 residues, 1 model selected > ui tool show ""Selection Inspector"" > setattr sel r ribbon_hide_backbone false Assigning ribbon_hide_backbone attribute to 4 items > show sel cartoons > ui tool show H-Bonds > hbonds sel color #000000 radius 0.05 dashes 4 restrict both interModel false > distSlop 0.6 angleSlop 40.0 select true reveal true 2 hydrogen bonds found > delete H ===== 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: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88 OpenGL renderer: Apple M1 Max 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: MacBookPro18,2 Model Number: Z14X000HSLL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 64 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: 22 days, 16 hours, 20 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 32 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina XDR Display Resolution: 3456 x 2234 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: No Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-Clipper: 0.22.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ISOLDE: 1.7.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Structure Editing can't reproduce Tom Goddard all ChimeraX