id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 18019 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-14.6.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. Fatal Python error: Segmentation fault Thread 0x0000000326343000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000325337000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032432b000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000032331f000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000322313000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000321307000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x00000003202fb000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031f2ef000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031e2e3000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031d2d7000 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File 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""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x00000001f7f84f40 (most recent call first): File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 330 in event_loop File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1054 in init File ""/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1217 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, 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2016-2024 Regents of the University of California. All rights reserved. > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/Footprints1A1_vs_6G1.cxs"" Log from Mon Dec 9 13:25:32 2024UCSF ChimeraX version: 1.8.dev202311280534 (2023-11-28) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/6G1/6G1_H_and_L.cxs"" Log from Thu Dec 5 12:26:01 2024UCSF ChimeraX version: 1.8.dev202311280534 (2023-11-28) © 2016-2023 Regents of the University of California. All rights reserved. > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/6G1/6G1.cxs"" Log from Wed Dec 4 17:01:57 2024 Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle UCSF ChimeraX version: 1.8.dev202311280534 (2023-11-28) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/ModelsFromPhilip/H5+12G1_coot-0-coot-32_real_space_refined_036.pdb"" Chain information for H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #1 --- Chain | Description A C | No description available B | No description available H | No description available L | No description available a b c | No description available > hide cartoons > hide atoms > show cartoons > set bgColor white > lighting soft > graphics silhouettes true > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 26163 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > select /B 4986 atoms, 5055 bonds, 316 residues, 1 model selected > color sel light grey > select clear > select /b:153 24 atoms, 23 bonds, 1 residue, 1 model selected > select up 2582 atoms, 2611 bonds, 165 residues, 1 model selected > select up 26421 atoms, 26767 bonds, 1685 residues, 1 model selected > select down 2582 atoms, 2611 bonds, 165 residues, 1 model selected > color sel light grey > select /c:87 7 atoms, 6 bonds, 1 residue, 1 model selected > select add /A:88 23 atoms, 21 bonds, 2 residues, 1 model selected > select up 7550 atoms, 7646 bonds, 481 residues, 1 model selected > select clear > select /c:90 12 atoms, 11 bonds, 1 residue, 1 model selected > select add /C:289 25 atoms, 23 bonds, 2 residues, 1 model selected > select up 7550 atoms, 7646 bonds, 481 residues, 1 model selected > color sel grey > select /a:97 15 atoms, 14 bonds, 1 residue, 1 model selected > select add /A:312 29 atoms, 27 bonds, 2 residues, 1 model selected > select up 7550 atoms, 7646 bonds, 481 residues, 1 model selected > color sel dark grey > select clear > select /C:280 22 atoms, 21 bonds, 1 residue, 1 model selected > select add /c:89 41 atoms, 39 bonds, 2 residues, 1 model selected > select up 7550 atoms, 7646 bonds, 481 residues, 1 model selected > color sel dark grey Drag select of 6 residues > select /a:93 14 atoms, 13 bonds, 1 residue, 1 model selected > select add /A:49 21 atoms, 19 bonds, 2 residues, 1 model selected > select up 7550 atoms, 7646 bonds, 481 residues, 1 model selected > color sel grey > select clear > select ::name=""NAG"" 258 atoms, 258 bonds, 12 residues, 1 model selected > show sel atoms > color sel byhetero > select clear Drag select of 168 atoms, 1256 residues, 170 bonds > select clear Drag select of 97 atoms, 599 residues, 97 bonds > select up 9676 atoms, 9757 bonds, 605 residues, 1 model selected > select up 9688 atoms, 9770 bonds, 605 residues, 1 model selected > select up 22697 atoms, 22989 bonds, 1445 residues, 1 model selected > show sel surfaces > select clear > select /L:41 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 1348 atoms, 1364 bonds, 87 residues, 1 model selected > select up 1709 atoms, 1730 bonds, 112 residues, 1 model selected > color sel light blue > select /H:20 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 95 atoms, 94 bonds, 7 residues, 1 model selected > select up 1867 atoms, 1894 bonds, 122 residues, 1 model selected > color sel blue > color sel dark blue > select /B:173@CB 1 atom, 1 residue, 1 model selected > select clear > select #1/H:32,100E,100G,96,100C,100E,100D,100B,100C,100B,100A,100B 142 atoms, 143 bonds, 8 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select H 12931 atoms, 1680 residues, 1 model selected > hide sel atoms > select clear > select #1/B:128 14 atoms, 14 bonds, 1 residue, 1 model selected > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/12G1.cxs"" includeMaps true > select #1/B 4986 atoms, 5055 bonds, 316 residues, 1 model selected > mlp sel Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_B SES surface"": minimum -26.4, mean -4.411, maximum 25.25 To also show corresponding color key, enter the above mlp command and add key true > select #1/B:125B 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/B:166 19 atoms, 18 bonds, 1 residue, 1 model selected > select /H:100F 21 atoms, 21 bonds, 1 residue, 1 model selected > select #1/B:126 11 atoms, 10 bonds, 1 residue, 1 model selected > ui tool show ""Side View"" > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/12G1_hydrophob_groove.png"" width > 965 height 830 supersample 4 transparentBackground true > save 12G1_hydrophob_groove.png supersample 8 transparentBackground true > mlp Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_A SES surface"": minimum -27.45, mean -4.283, maximum 24.92 Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_B SES surface"": minimum -26.4, mean -4.411, maximum 25.25 Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_C SES surface"": minimum -26.09, mean -4.143, maximum 25.32 Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_H SES surface"": minimum -27.55, mean -4.03, maximum 24.65 Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_L SES surface"": minimum -24.86, mean -2.588, maximum 24.9 Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_a SES surface"": minimum -27.38, mean -3.167, maximum 24.57 Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_b SES surface"": minimum -28.19, mean -3.158, maximum 24.83 Map values for surface ""H5+12G1_coot-0-coot-32_real_space_refined_036.pdb_c SES surface"": minimum -26.9, mean -3.236, maximum 23.26 To also show corresponding color key, enter the above mlp command and add key true > undo > hide surfaces Drag select of 8 atoms, 425 residues, 7 bonds > select /B:147 20 atoms, 20 bonds, 1 residue, 1 model selected Drag select of 21 atoms, 507 residues, 22 bonds > select up 8187 atoms, 8263 bonds, 510 residues, 7 models selected > select up 8205 atoms, 8282 bonds, 510 residues, 7 models selected > select up 22628 atoms, 22916 bonds, 1441 residues, 7 models selected > select up 22845 atoms, 23143 bonds, 1451 residues, 7 models selected > select up 26421 atoms, 26767 bonds, 1685 residues, 7 models selected > select down 22845 atoms, 23143 bonds, 1451 residues, 9 models selected > show sel surfaces > select /B:122@CD1 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 2 models selected > select up 4905 atoms, 4970 bonds, 312 residues, 2 models selected > color (#!1 & sel) light gray > select clear > select /C:25@H 1 atom, 1 residue, 1 model selected > select add /C:273@CB 2 atoms, 2 residues, 2 models selected > select up 32 atoms, 30 bonds, 2 residues, 2 models selected > select up 4968 atoms, 5035 bonds, 316 residues, 2 models selected > select up 5063 atoms, 5134 bonds, 320 residues, 2 models selected > select up 26421 atoms, 26767 bonds, 1685 residues, 2 models selected > select down 5063 atoms, 5134 bonds, 320 residues, 9 models selected > color (#!1 & sel) gray > select /a:14@NE1 1 atom, 1 residue, 1 model selected > select add /A:285@HB 2 atoms, 2 residues, 2 models selected > select up 40 atoms, 40 bonds, 2 residues, 3 models selected > select up 7550 atoms, 7646 bonds, 481 residues, 3 models selected > select up 7632 atoms, 7732 bonds, 485 residues, 3 models selected > select up 26421 atoms, 26767 bonds, 1685 residues, 3 models selected > select down 7632 atoms, 7732 bonds, 485 residues, 9 models selected > color (#!1 & sel) dim gray > select clear > select /c:34@CE1 1 atom, 1 residue, 1 model selected > select add /C:44@OE1 2 atoms, 2 residues, 2 models selected > select up 36 atoms, 35 bonds, 2 residues, 3 models selected > select up 7550 atoms, 7646 bonds, 481 residues, 3 models selected > select up 7645 atoms, 7745 bonds, 485 residues, 3 models selected > ui tool show ""Color Actions"" > color (#!1 & sel) #919191ff > select clear > select /H:48 19 atoms, 18 bonds, 1 residue, 1 model selected > select up 700 atoms, 714 bonds, 44 residues, 2 models selected > select up 1867 atoms, 1894 bonds, 122 residues, 2 models selected > hide sel atoms > select clear > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/ModelsFromPhilip/H5_6G1-coot-11_renumbered_real_space_refined_018.pdb"" Chain information for H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1 --- Chain | Description A B C | No description available H | No description available L | No description available a b c | No description available > hide atoms > show cartoons > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 26126 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > lighting soft > graphics silhouettes false > graphics silhouettes true > select /A:275 7 atoms, 6 bonds, 1 residue, 1 model selected > select add /a:45 26 atoms, 24 bonds, 2 residues, 1 model selected > select up 3391 atoms, 3432 bonds, 216 residues, 1 model selected > select up 7653 atoms, 7752 bonds, 484 residues, 1 model selected > color sel light grey > select /b:97 15 atoms, 14 bonds, 1 residue, 1 model selected > select add /B:300 34 atoms, 32 bonds, 2 residues, 1 model selected > select up 1623 atoms, 1638 bonds, 101 residues, 1 model selected > select up 7638 atoms, 7738 bonds, 484 residues, 1 model selected > color sel tin Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > select clear > select /B:21 13 atoms, 12 bonds, 1 residue, 1 model selected > select add /b:93 27 atoms, 25 bonds, 2 residues, 1 model selected > select up 1676 atoms, 1686 bonds, 104 residues, 1 model selected > select up 7638 atoms, 7738 bonds, 484 residues, 1 model selected > color sel #929292ff > color sel #919191ff > select /c:86 12 atoms, 11 bonds, 1 residue, 1 model selected > select add /C:285 28 atoms, 26 bonds, 2 residues, 1 model selected > select up 4886 atoms, 4949 bonds, 305 residues, 1 model selected > select up 7640 atoms, 7739 bonds, 484 residues, 1 model selected > color sel dim gray > select clear > select /H:8 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 213 atoms, 214 bonds, 15 residues, 1 model selected > select up 1900 atoms, 1928 bonds, 125 residues, 1 model selected > color sel #009051ff > color sel #008f00ff > color sel #4f8f00ff > color sel #009051ff > select /L:41 7 atoms, 6 bonds, 1 residue, 1 model selected > select up 1674 atoms, 1696 bonds, 111 residues, 1 model selected > select up 26505 atoms, 26853 bonds, 1688 residues, 1 model selected > select down 1674 atoms, 1696 bonds, 111 residues, 1 model selected > color sel #00f900ff > color sel #00fa92ff > color sel #8efa00ff > color sel #73fa79ff > color sel lime > select clear > select ::name=""NAG"" 379 atoms, 379 bonds, 15 residues, 1 model selected > show sel atoms > color sel byhetero Drag select of 78 residues > select up 15409 atoms, 15587 bonds, 961 residues, 1 model selected > select up 22931 atoms, 23229 bonds, 1452 residues, 1 model selected > show sel surfaces > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/6G1.cxs"" includeMaps true ——— End of log from Wed Dec 4 17:01:57 2024 ——— opened ChimeraX session > select > #1/H:100C,100C,31,32,100E,100G,101,96,101,100G,100E,100E,100G,100D,100B,100C,100B,100B 148 atoms, 146 bonds, 9 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select /A:125@CG 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 2 models selected > select up 221 atoms, 223 bonds, 12 residues, 2 models selected > select up 4285 atoms, 4343 bonds, 269 residues, 2 models selected > mlp sel Map values for surface ""H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_A SES surface"": minimum -26.3, mean -4.312, maximum 25.79 To also show corresponding color key, enter the above mlp command and add key true > select clear > save 6G1_H_A_hydrophobicGrooveFromRight.png supersample 8 > transparentBackground true > save 6G1_H_A_hydrophobicGrooveFromLeft.png supersample 8 > transparentBackground true > select H 12980 atoms, 1686 residues, 1 model selected > hide sel atoms > select clear > save 6G1_H_A_hydrophobicGrooveHeadOn.png supersample 8 transparentBackground > true > select clear > select #1/L:57,49,56,49,30,50,28,28,28,28,53,28 111 atoms, 109 bonds, 7 residues, 1 model selected > show sel atoms > color sel byhetero > select H 12980 atoms, 1686 residues, 1 model selected > hide sel atoms > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/6G1/6G1_H_and_L.cxs"" includeMaps > true ——— End of log from Thu Dec 5 12:26:01 2024 ——— opened ChimeraX session > select clear Drag select of H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_A SES surface, 51162 of 345860 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_B SES surface, 129488 of 352546 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_C SES surface, 106496 of 351158 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_a SES surface, 103612 of 239464 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_b SES surface, 89353 of 244122 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_c SES surface, 106063 of 233634 triangles, 110 atoms, 497 residues, 112 bonds > select up 7812 atoms, 7876 bonds, 505 residues, 7 models selected > select up 7890 atoms, 7954 bonds, 505 residues, 7 models selected > select up 16851 atoms, 17042 bonds, 1068 residues, 7 models selected > select up 22931 atoms, 23229 bonds, 1452 residues, 7 models selected > show sel surfaces > ui tool show ""Side View"" > hide sel surfaces > select clear Drag select of 129 atoms, 596 residues, 128 bonds > select up 9407 atoms, 9491 bonds, 606 residues, 7 models selected > select up 17313 atoms, 17513 bonds, 1097 residues, 7 models selected > select up 22931 atoms, 23229 bonds, 1452 residues, 7 models selected > ui tool show ""Color Actions"" > open /Users/aleon/Desktop/Jiangsu_RTH_gisAID_H5_alignment.aln-clustalw Unrecognized file suffix '.aln-clustalw' > open /Users/aleon/Desktop/Jiangsu_RTH_gisAID_H5_alignment.aln Summary of feedback from opening /Users/aleon/Desktop/Jiangsu_RTH_gisAID_H5_alignment.aln --- notes | Alignment identifier is Jiangsu_RTH_gisAID_H5_alignment.aln Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Showing conservation header (""seq_conservation"" residue attribute) for alignment Jiangsu_RTH_gisAID_H5_alignment.aln Opened 808 sequences from Jiangsu_RTH_gisAID_H5_alignment.aln > color sel byattr seq_conservation palette royal blue:pale turquoise:light > grey Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel byattr seq_conservation Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel by seq_conservation Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color sel byattr seq_conservation Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color byattribute seq_conservation 26505 atoms, 1688 residues, 6 surfaces, atom seq_conservation range -5.46 to 0.353 Fetching compressed palette royal from https://www.colourlovers.com/api/palettes?keywords=royal&format=json&numResults=100 Could not find palette royal at COLOURlovers.com using keyword search > color byattribute seq_conservation palette snow:moccasin:navy 26505 atoms, 1688 residues, 6 surfaces, atom seq_conservation range -5.46 to 0.353 > toolshed show > color byattribute seq_conservation palette cyanmaroon key true > key cyan-white-maroon :-5.461 :-2.554 :0.353 showTool true > ui mousemode right ""color key"" 26505 atoms, 1688 residues, 6 surfaces, atom seq_conservation range -5.46 to 0.353 > key cyan-white-maroon :-5.461 "":\\\"" :0.353 > key cyan-white-maroon :-5.461 : :0.353 > key cyan-white-maroon :-5.461 : :C > key cyan-white-maroon :-5.461 : :Co > key cyan-white-maroon :-5.461 : :Con > key cyan-white-maroon :-5.461 : :Cons > key cyan-white-maroon :-5.461 : :Conse > key cyan-white-maroon :-5.461 : :Conser > key cyan-white-maroon :-5.461 : :Conserv > key cyan-white-maroon :-5.461 : :Conserve > key cyan-white-maroon :-5.461 : :Conserver > key cyan-white-maroon :-5.461 : :Conserverd > key cyan-white-maroon :-5.461 : :Conserver > key cyan-white-maroon :-5.461 : :Conserve > key cyan-white-maroon :-5.461 : :Conserved > key cyan-white-maroon :V : :Conserved > key cyan-white-maroon : : :Conserved > key cyan-white-maroon :V : :Conserved > key cyan-white-maroon :Va : :Conserved > key cyan-white-maroon :Var : :Conserved > key cyan-white-maroon :Vari : :Conserved > key cyan-white-maroon :Varia : :Conserved > key cyan-white-maroon :Variab : :Conserved > key cyan-white-maroon :Variabl : :Conserved > key cyan-white-maroon :Variable : :Conserved > key ^cyan-white-maroon :Conserved : :Variable > key labelColor #bfbfbf > key labelColor default > select /A-C:125B 33 atoms, 30 bonds, 3 residues, 1 model selected > select /A-C:125B-126 66 atoms, 63 bonds, 6 residues, 1 model selected > select /A:131 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A:132 14 atoms, 13 bonds, 1 residue, 1 model selected > select /A:131 15 atoms, 14 bonds, 1 residue, 1 model selected > select /A-C:132 42 atoms, 39 bonds, 3 residues, 1 model selected > select /A-C:132 42 atoms, 39 bonds, 3 residues, 1 model selected > select /C:125B 11 atoms, 10 bonds, 1 residue, 1 model selected > select /A:169 13 atoms, 12 bonds, 1 residue, 1 model selected > select /A:166 /B:166 /C:166 57 atoms, 54 bonds, 3 residues, 1 model selected > select /A:169 /B:169 /C:169 39 atoms, 36 bonds, 3 residues, 1 model selected > select /A:168 /B:168 /C:168 63 atoms, 63 bonds, 3 residues, 1 model selected > select clear > key spectral-3 :Conserved : :Variable > key accent-3 :Conserved : :Variable > key blues-3 :Conserved : :Variable > color byattribute seq_conservation palette blues key true > key blues :-5.461 :-4.008 :-2.554 :-1.101 :0.353 showTool true 26505 atoms, 1688 residues, 6 surfaces, atom seq_conservation range -5.46 to 0.353 > key gnbu-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key greys-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key paired-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key paecontacts :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key pastel2-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key piyg-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key prgn-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key pubu :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key prgn-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key set3-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key set1-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key ylorrd :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key spectral :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key spectral-5 :-5.461 :-4.008 :-2.554 :-1.101 :0.353 [Repeated 1 time(s)] > key esmfold :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key blues :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > key greys :-5.461 :-4.008 :-2.554 :-1.101 :0.353 > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/SequenceConservation.cxs"" > includeMaps true > close all > ui mousemode right translate > open /Users/aleon/Downloads/H5_1A1.pdb Chain information for H5_1A1.pdb #1 --- Chain | Description A B C | No description available H | No description available L | No description available a b c | No description available Associated H5_1A1.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain c to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Drag select of 26476 atoms, 394 bonds > select up 26505 atoms, 26853 bonds, 1688 residues, 1 model selected > hide sel atoms > show sel cartoons > show sel surfaces > select /L:83@HG21 1 atom, 1 residue, 1 model selected > select add /H:108@O 2 atoms, 2 residues, 2 models selected > select up 30 atoms, 29 bonds, 2 residues, 3 models selected > select up 2614 atoms, 2646 bonds, 173 residues, 3 models selected > hide sel surfaces > select /H:10@N 1 atom, 1 residue, 1 model selected > select up 7 atoms, 6 bonds, 1 residue, 2 models selected > select up 213 atoms, 214 bonds, 15 residues, 2 models selected > select up 1900 atoms, 1928 bonds, 125 residues, 2 models selected > hide sel surfaces > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/ModelsFromPhilip/H5_6G1-coot-11_renumbered_real_space_refined_018.pdb"" Chain information for H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #2 --- Chain | Description A B C | No description available H | No description available L | No description available a b c | No description available Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain c to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches > select add #2 28405 atoms, 28781 bonds, 1813 residues, 3 models selected > select add #1 53010 atoms, 53706 bonds, 3376 residues, 3 models selected > select subtract #1 26505 atoms, 26853 bonds, 1688 residues, 9 models selected > select clear > select add #2 26505 atoms, 26853 bonds, 1688 residues, 1 model selected > hide sel atoms > show sel cartoons > select clear > select #1/A:278@HA 1 atom, 1 residue, 1 model selected > select add #1/a:38@CD 2 atoms, 2 residues, 2 models selected > select up 36 atoms, 34 bonds, 2 residues, 3 models selected > select up 3391 atoms, 3432 bonds, 216 residues, 3 models selected > select up 7653 atoms, 7752 bonds, 484 residues, 3 models selected > color sel light grey > select #1/b:14@CE3 1 atom, 1 residue, 1 model selected > select add #1/B:22@OG 2 atoms, 2 residues, 2 models selected > select up 35 atoms, 35 bonds, 2 residues, 3 models selected > select up 1326 atoms, 1340 bonds, 90 residues, 3 models selected > select up 7638 atoms, 7738 bonds, 484 residues, 3 models selected > color sel dark grey > select #1/c:34@CE1 1 atom, 1 residue, 1 model selected > select add #1/C:292@CE 2 atoms, 2 residues, 2 models selected > select up 38 atoms, 37 bonds, 2 residues, 3 models selected > select up 4536 atoms, 4603 bonds, 291 residues, 3 models selected > select up 7640 atoms, 7739 bonds, 484 residues, 3 models selected > color sel grey > select clear > select #2/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > ui tool show ""Color Actions"" > color sel #009051ff > select clear > select #1/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > color (#!1 & sel) #ff2600ff > color (#!1 & sel) red > select clear > select #1/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > ui tool show ""Color Actions"" > ui tool show ""Color Zone"" No surface chosen for color zoning > select sel : select sel : select #1/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > select sel : select clear > select #2/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > select sel : select #2/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > select sel : select #2/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > select sel : select #1/B:51@CD1 1 atom, 1 residue, 1 model selected > select add #1/b:28@N 2 atoms, 2 residues, 2 models selected > select up 33 atoms, 31 bonds, 2 residues, 3 models selected > select up 1326 atoms, 1340 bonds, 90 residues, 3 models selected > select up 7638 atoms, 7738 bonds, 484 residues, 3 models selected > color sel tin Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > ui tool show ""Color Actions"" > color (#!1 & sel) #919191ff > select #1/c:15@NE2 1 atom, 1 residue, 1 model selected > select add #1/C:60@CG2 2 atoms, 2 residues, 2 models selected > select up 36 atoms, 34 bonds, 2 residues, 3 models selected > select up 1327 atoms, 1341 bonds, 90 residues, 3 models selected > select up 7640 atoms, 7739 bonds, 484 residues, 3 models selected > color sel dim grey > select clear > select sel : select #2/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > select sel : color (#!1-2 & sel) #009051ff > select #1/H/L 3574 atoms, 3624 bonds, 236 residues, 1 model selected > color sel red > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/Footprints1A1_vs_6G1.cxs"" > includeMaps true ——— End of log from Mon Dec 9 13:25:32 2024 ——— opened ChimeraX session > lighting soft > select clear > select #1/A-C:13-321/a-c:2-166 #2/A-C:13-321/a-c:2-166 45104 atoms, 45670 bonds, 2874 residues, 2 models selected > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/ForGarazi/EditsDec18AL/H5_final.aln"" Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre Leon/Flu Andre/GaraziH5/ForGarazi/EditsDec18AL/H5_final.aln --- notes | Alignment identifier is H5_final.aln Associated H5_1A1.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_1A1.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Showing conservation header (""seq_conservation"" residue attribute) for alignment H5_final.aln Opened 18 sequences from H5_final.aln > select clear > select #1/B:274@N 1 atom, 1 residue, 1 model selected > select up 20 atoms, 20 bonds, 1 residue, 2 models selected > select up 772 atoms, 781 bonds, 51 residues, 2 models selected > select up 5030 atoms, 5100 bonds, 318 residues, 2 models selected > select up 26505 atoms, 26853 bonds, 1688 residues, 2 models selected > select down 5030 atoms, 5100 bonds, 318 residues, 9 models selected > select #1/b:32@HG 1 atom, 1 residue, 1 model selected > select add #1/B:292@SD 2 atoms, 2 residues, 2 models selected > select up 28 atoms, 26 bonds, 2 residues, 3 models selected > select up 1273 atoms, 1292 bonds, 87 residues, 3 models selected > select up 7638 atoms, 7738 bonds, 484 residues, 3 models selected > color sel grey > select #1/a:42@NE2 1 atom, 1 residue, 1 model selected > select add #1/A:304@OE2 2 atoms, 2 residues, 2 models selected > select up 32 atoms, 30 bonds, 2 residues, 3 models selected > select up 3391 atoms, 3432 bonds, 216 residues, 3 models selected > select up 7653 atoms, 7752 bonds, 484 residues, 3 models selected > color sel light grey grey Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > select clear Drag select of 16 residues > select up 1674 atoms, 1696 bonds, 111 residues, 2 models selected > select up 26505 atoms, 26853 bonds, 1688 residues, 2 models selected > select down 1674 atoms, 1696 bonds, 111 residues, 9 models selected > select clear > select #1/H:13 22 atoms, 21 bonds, 1 residue, 1 model selected > select add #1/L:10 33 atoms, 31 bonds, 2 residues, 2 models selected > select up 1887 atoms, 1910 bonds, 126 residues, 3 models selected > select up 3574 atoms, 3624 bonds, 236 residues, 3 models selected > color sel #FFBF00 > select clear > select #1/B:51@CD1 1 atom, 1 residue, 1 model selected > select #1/b:34@CZ 1 atom, 1 residue, 1 model selected > select add #1/B:57@NZ 2 atoms, 2 residues, 2 models selected > select up 43 atoms, 42 bonds, 2 residues, 3 models selected > select up 1326 atoms, 1340 bonds, 90 residues, 3 models selected > select up 7638 atoms, 7738 bonds, 484 residues, 3 models selected > color sel grey > select #1/B:142@C 1 atom, 1 residue, 1 model selected > select clear > select add #1/H:62 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #1/L:14 25 atoms, 23 bonds, 2 residues, 2 models selected > select up 1718 atoms, 1740 bonds, 114 residues, 3 models selected > select up 3574 atoms, 3624 bonds, 236 residues, 3 models selected > ui tool show ""Surface Color"" > select sel @ select sel @ color sel #FFBF00 > select clear > select #1/L:3 16 atoms, 15 bonds, 1 residue, 1 model selected > select add #1/H:62 27 atoms, 25 bonds, 2 residues, 2 models selected > select up 1718 atoms, 1740 bonds, 114 residues, 3 models selected > select up 3574 atoms, 3624 bonds, 236 residues, 3 models selected > select sel : color sel #FFBF00 > select clear > select ::name=""NAG"" 758 atoms, 758 bonds, 30 residues, 2 models selected > show sel atoms > color sel byhetero > select clear Drag select of 164 residues > select up 5248 atoms, 5319 bonds, 347 residues, 4 models selected > select up 7148 atoms, 7248 bonds, 472 residues, 4 models selected > hide > ~hide Unknown command: ~hide > select clear Drag select of 80 residues > select down 1154 atoms, 80 residues, 3 models selected > select up 5050 atoms, 5118 bonds, 334 residues, 3 models selected > select up 5248 atoms, 5320 bonds, 347 residues, 3 models selected > select up 53010 atoms, 53706 bonds, 3376 residues, 3 models selected > select down 5248 atoms, 5320 bonds, 347 residues, 10 models selected > select clear Drag select of 215 residues > select up 7069 atoms, 7167 bonds, 467 residues, 4 models selected > select up 7148 atoms, 7248 bonds, 472 residues, 4 models selected > hide sel cartoons > center Unknown command: center > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/H5_Footprints.cxs"" includeMaps true > close > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/20D10/20D10.cxs"" opened ChimeraX session > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/12G1/12G1_all_residues.cxs"" opened ChimeraX session Drag select of 62 residues > select up 3047 atoms, 3089 bonds, 200 residues, 1 model selected > select down 886 atoms, 62 residues, 1 model selected > select down 886 atoms, 62 residues, 1 model selected > select clear > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/20D10/20D10.cxs"" opened ChimeraX session > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/overlays/Overlays_HCDRs_shown_noH.cxs"" opened ChimeraX session > show #2 models > show #!3 models > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/1A1_overlay/H5_1A1.pdb"" Chain information for H5_1A1.pdb #4 --- Chain | Description A B C | No description available H | No description available L | No description available a b c | No description available > select clear > hide #!1 models > hide #2 models > hide #!3 models > select add #4 26505 atoms, 26853 bonds, 1688 residues, 1 model selected > hide sel atoms > show sel cartoons > select clear Drag select of 943 residues > select up 19538 atoms, 19766 bonds, 1242 residues, 1 model selected > select up 22931 atoms, 23229 bonds, 1452 residues, 1 model selected > color sel grey > select clear > select #4/b:119 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #4/B:258 42 atoms, 42 bonds, 2 residues, 1 model selected > select up 904 atoms, 910 bonds, 53 residues, 1 model selected > select up 7638 atoms, 7738 bonds, 484 residues, 1 model selected > color sel light grey > select clear Drag select of 146 residues > select up 3574 atoms, 3624 bonds, 236 residues, 1 model selected > color sel #FFBF00 > select clear > show #!3 models > show #2 models > show #!1 models > hide #!1 models > hide #2 models > hide #!3 models > hide #4 models > show #!1 models > show #2 models > show #!3 models Drag select of 233 residues > select up 9754 atoms, 9886 bonds, 642 residues, 3 models selected > select up 10699 atoms, 10845 bonds, 704 residues, 3 models selected > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #2#!1,3 atoms > select clear Drag select of 211 residues > select up 9706 atoms, 9838 bonds, 639 residues, 3 models selected > select up 10699 atoms, 10845 bonds, 704 residues, 3 models selected > hide sel atoms > show sel cartoons > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 26126 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > hide #!3 models > hide #2 models Drag select of 91 atoms, 674 residues, 90 bonds > select up 21558 atoms, 21790 bonds, 1386 residues, 9 models selected > select up 21656 atoms, 21891 bonds, 1386 residues, 9 models selected > select up 29336 atoms, 29703 bonds, 1884 residues, 9 models selected > select up 33630 atoms, 34074 bonds, 2156 residues, 9 models selected > select clear Drag select of 127 atoms, 808 residues, 128 bonds > select up 12863 atoms, 12978 bonds, 818 residues, 7 models selected > select up 12978 atoms, 13095 bonds, 818 residues, 7 models selected > select up 19098 atoms, 19328 bonds, 1209 residues, 7 models selected > select up 22931 atoms, 23229 bonds, 1452 residues, 7 models selected > show sel surfaces > select clear > show #2 models > show #!3 models > show #4 models > hide #4 models > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/overlays_Ribbon_slab_noH_noSCs.cxs"" includeMaps > true > show #4 models > hide #4 models > hide #!3 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #!1 models > select #2/a:46 12 atoms, 11 bonds, 1 residue, 1 model selected > select add #2/A:119 27 atoms, 25 bonds, 2 residues, 1 model selected > select up 404 atoms, 403 bonds, 25 residues, 1 model selected > select up 7658 atoms, 7758 bonds, 485 residues, 1 model selected > color sel light grey > select add #2/b:90 7670 atoms, 7769 bonds, 486 residues, 1 model selected > select clear > select add #2/b:90 12 atoms, 11 bonds, 1 residue, 1 model selected > select add #2/c:86 24 atoms, 22 bonds, 2 residues, 1 model selected > select add #2/B:179 43 atoms, 40 bonds, 3 residues, 1 model selected > select add #2/C:148 54 atoms, 50 bonds, 4 residues, 1 model selected > select up 2360 atoms, 2383 bonds, 142 residues, 1 model selected > select up 15315 atoms, 15515 bonds, 970 residues, 1 model selected > color sel grey > select clear Drag select of 356 residues > select up 10972 atoms, 11070 bonds, 703 residues, 1 model selected > select up 22973 atoms, 23273 bonds, 1455 residues, 1 model selected > show sel surfaces > select clear > select ::name=""NAG"" 1340 atoms, 1340 bonds, 54 residues, 4 models selected > show sel & #!2 atoms > color sel & #!2 byhetero > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!2 atoms > select clear > show #!3 models > show #!1 models > select add #1 26505 atoms, 26853 bonds, 1688 residues, 1 model selected > hide sel surfaces > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/overlays_Ribbon_slab_noH_noSCs.cxs"" includeMaps > true > hide #!3 models > show #!3 models > hide #!2 models > hide #!1 models Drag select of 243 residues > select up 14841 atoms, 15040 bonds, 944 residues, 1 model selected > hide sel cartoons > show #!2 models > show #!1 models > hide #!2 models Drag select of 3 atoms, 273 residues, 2 bonds > select up 4404 atoms, 4446 bonds, 274 residues, 4 models selected > select up 10420 atoms, 10568 bonds, 659 residues, 4 models selected > select up 15107 atoms, 15315 bonds, 954 residues, 4 models selected > hide sel cartoons > select clear > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > hide #!1 models > show #!2 models > show #!1 models > select add #1 26505 atoms, 26853 bonds, 1688 residues, 1 model selected > select add #3 52926 atoms, 53620 bonds, 3373 residues, 8 models selected > hide sel atoms > select clear > select #1/H:1-95 1490 atoms, 1510 bonds, 98 residues, 1 model selected > transparency sel 75 cartoons > select #2/H:1-95 1467 atoms, 1486 bonds, 97 residues, 1 model selected > transparency sel 75 cartoons > select #3/H:1-95 1499 atoms, 1519 bonds, 98 residues, 1 model selected > transparency sel 75 cartoons > select clear > select #3/H:100H-113 167 atoms, 168 bonds, 12 residues, 1 model selected > transparency sel 75 cartoons > select #2/H:100H-113 185 atoms, 186 bonds, 13 residues, 1 model selected > transparency sel 75 cartoons > select #1/H:100H-113 204 atoms, 206 bonds, 15 residues, 1 model selected > select #1/H:100I-113 197 atoms, 199 bonds, 14 residues, 1 model selected > transparency sel 75 cartoons > select clear > select #1/L:1-17 236 atoms, 238 bonds, 16 residues, 1 model selected > select #1/L:127 Nothing selected > select #1/L:1-27 372 atoms, 375 bonds, 26 residues, 1 model selected > transparency sel 75 cartoons > select #2/L:1-27 389 atoms, 392 bonds, 27 residues, 1 model selected > transparency sel 75 cartoons > select #3/L:1-27 389 atoms, 392 bonds, 27 residues, 1 model selected > transparency sel 75 cartoons > select #3/L:33-113 1154 atoms, 1166 bonds, 75 residues, 1 model selected > transparency sel 75 cartoons > select #2/L:33-113 1164 atoms, 1178 bonds, 75 residues, 1 model selected > transparency sel 75 cartoons > select up 1712 atoms, 1734 bonds, 112 residues, 1 model selected > select clear > select #1/L:33-113 1151 atoms, 1165 bonds, 75 residues, 1 model selected > transparency sel 75 cartoons > select clear > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > lighting shadows true intensity 0.5 > lighting shadows false > lighting shadows true > lighting shadows false > lighting soft > graphics silhouettes false > graphics silhouettes true > graphics silhouettes false > graphics silhouettes true > save overlay_zoom_H5.png supersample 8 transparentBackground true > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/overlays_Ribbon_slab_noH_noSCs_transparencies.cxs"" > includeMaps true > hide #!3 models > hide #!2 models > select add #1 26505 atoms, 26853 bonds, 1688 residues, 1 model selected > show sel cartoons > select clear > preset cartoons/nucleotides ribbons/slabs Using preset: Cartoons/Nucleotides / Ribbons/Slabs Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect nucleotides tube/slab shape box > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > select #1/H:32,96,100B,100C,100E 90 atoms, 88 bonds, 5 residues, 1 model selected > show sel atoms > color sel byhetero > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!1 atoms > select clear > ~transparency Unknown command: ~transparency > transparency all - Missing or invalid ""percent"" argument: Expected a number > transparency all 0 > transparency all c 0 Missing or invalid ""percent"" argument: Expected a number > transparency all 0 cartoons Drag select of 102 residues > select up 3539 atoms, 3589 bonds, 234 residues, 1 model selected > select up 3574 atoms, 3624 bonds, 236 residues, 1 model selected > select down 3539 atoms, 3589 bonds, 234 residues, 1 model selected > select up 3574 atoms, 3624 bonds, 236 residues, 1 model selected > hide sel cartoons > select #1/H:95-100H,30-34 313 atoms, 320 bonds, 19 residues, 1 model selected > show sel cartoons > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol > false intraRes false reveal true retainCurrent true 7 hydrogen bonds found > select clear > select #1/L:32@CZ 1 atom, 1 residue, 1 model selected > select add #1/H:97@CD 2 atoms, 2 residues, 1 model selected > select add #1/H:100F@CD2 3 atoms, 3 residues, 1 model selected > select add #1/L:34@CG 4 atoms, 4 residues, 1 model selected > select subtract #1/L:34@CG 3 atoms, 3 residues, 1 model selected > select add #1/L:34@CG 4 atoms, 4 residues, 1 model selected > select add #1/L:32@CG 5 atoms, 4 residues, 1 model selected > select up 78 atoms, 76 bonds, 4 residues, 1 model selected > select up 2614 atoms, 2646 bonds, 173 residues, 1 model selected > select down 78 atoms, 76 bonds, 4 residues, 1 model selected > hide sel atoms > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 10 atoms, 9 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/H:100E 21 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms > select #1/A:125B,128,169,124,167 68 atoms, 64 bonds, 5 residues, 1 model selected > show sel atoms > color sel byhetero > select clear > select #1/H:32@HH 1 atom, 1 residue, 1 model selected > hide sel atoms > undo > select clear > select #1/H:100C@CD1 1 atom, 1 residue, 1 model selected > select add #1/H:100C@CD1 1 atom, 1 bond, 1 residue, 1 model selected > ui tool show Distances > select add #1/A:124@CG1 2 atoms, 1 bond, 2 residues, 1 model selected > distance #1/H:100C@CD1 #1/A:124@CG1 Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/H LEU 100C CD1 and /A ILE 124 CG1: 5.076 > distance style color #ffd479 > select clear > distance style color #73fdff > distance style color #76d6ff > distance style color #73fdff > distance style color #00fdff > select #1/H:96@CG 1 atom, 1 residue, 1 model selected > select add #1/A:128@CG 2 atoms, 2 residues, 1 model selected > distance #1/H:96@CG #1/A:128@CG Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/H LEU 96 CG and /A PRO 128 CG: 3.739 > distance style color #73fdff > distance style color #00fdff > select clear > select H 51907 atoms, 6741 residues, 4 models selected > select clear > select #1/H:32@OH 1 atom, 1 residue, 1 model selected > select add #1/A:125B 12 atoms, 10 bonds, 2 residues, 1 model selected Exactly two atoms must be selected! > select #1/A:125B 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/A:125B@O 1 atom, 1 residue, 1 model selected > select add #1/H:32@OH 2 atoms, 2 residues, 2 models selected > distance #1/A:125B@O #1/H:32@OH Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/A SER 125B O and /H TYR 32 OH: 3.186 > select add #1/A:125B@CA 3 atoms, 2 residues, 2 models selected > select #1/A:125B@CA 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > select up 44 atoms, 43 bonds, 3 residues, 2 models selected > show sel cartoons > select #1/H:100D 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #1/A:167 25 atoms, 23 bonds, 2 residues, 1 model selected > hide sel cartoons > select #1/H:100D@O 1 atom, 1 residue, 1 model selected > select add #1/A:167@N 2 atoms, 2 residues, 1 model selected > distance #1/H:100D@O #1/A:167@N Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/H ASN 100D O and /A SER 167 N: 2.867 > select add #1/A:167@CB 1 atom, 1 bond, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 2 models selected > select up 25 atoms, 23 bonds, 2 residues, 2 models selected > show sel cartoons > select #1/A:169 13 atoms, 12 bonds, 1 residue, 1 model selected > select add #1/H:100B 23 atoms, 21 bonds, 2 residues, 2 models selected > hide sel cartoons > select #1/H:100B@O 1 atom, 1 residue, 1 model selected > select add #1/A:169@H 2 atoms, 2 residues, 1 model selected > select add #1/A:169@N 3 atoms, 2 residues, 2 models selected > select subtract #1/A:169@H 2 atoms, 2 residues, 2 models selected > distance #1/H:100B@O #1/A:169@N Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/H ALA 100B O and /A ASN 169 N: 2.933 > select up 4 atoms, 2 bonds, 2 residues, 1 model selected > select up 23 atoms, 21 bonds, 2 residues, 2 models selected > show sel cartoons > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!1 atoms > select clear > label delete > show #!2 models > hide #!2 models > show #!2 models > hide #!1 models > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5.cxs"" includeMaps true Drag select of 71 residues > select up 3283 atoms, 3327 bonds, 216 residues, 1 model selected > hide sel cartoons Drag select of 14 residues > select up 3549 atoms, 3597 bonds, 234 residues, 1 model selected > select up 26522 atoms, 26870 bonds, 1689 residues, 1 model selected > select down 3549 atoms, 3597 bonds, 234 residues, 7 models selected > hide sel cartoons > select clear > select #2/H:32,96,100A,100B,100C,100F 115 atoms, 115 bonds, 6 residues, 1 model selected > show sel atoms > select #2/A:125B,128,169,124,167,164 87 atoms, 82 bonds, 6 residues, 1 model selected > show sel atoms > select up 536 atoms, 542 bonds, 33 residues, 2 models selected > select clear > select #2/H:95-100H,30-34 305 atoms, 312 bonds, 19 residues, 1 model selected > show sel cartoons > select #2/H:32,96,100A,100B,100C,100F 115 atoms, 115 bonds, 6 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol > false intraRes false reveal true retainCurrent true 5 hydrogen bonds found > select #2/A:163 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 21 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms Unsupported scale factor (0.000000) detected on Display1 > select #2/A:167 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #2/H:100C 32 atoms, 31 bonds, 2 residues, 2 models selected > hide sel cartoons > select #2/A:167@O 1 atom, 1 residue, 1 model selected > select add #2/H:100C@N 2 atoms, 1 bond, 2 residues, 2 models selected > distance #2/A:167@O #2/H:100C@N Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/A SER 167 O and /H TYR 100C N: 3.145 > select #2/A:167@CA 1 atom, 1 residue, 1 model selected Drag select of 8 residues > select clear > select add #2/H:100C@H 1 atom, 1 bond, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > select up 32 atoms, 31 bonds, 2 residues, 2 models selected > show sel cartoons Drag select of 5 residues > select #2/B:96 19 atoms, 18 bonds, 1 residue, 1 model selected > select clear Drag select of 1 residues > select clear > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > select #2/H:100C 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #2/A:167 32 atoms, 31 bonds, 2 residues, 1 model selected > hide sel cartoons > show sel cartoons > select clear > select #2/A:169 13 atoms, 12 bonds, 1 residue, 1 model selected > select add #2/H:100A 27 atoms, 26 bonds, 2 residues, 2 models selected > hide sel cartoons > select #2/A:169@H 1 atom, 1 residue, 1 model selected > select add #2/H:100A@O 2 atoms, 2 residues, 2 models selected > select add #2/A:169@N 3 atoms, 2 residues, 2 models selected > select subtract #2/A:169@H 2 atoms, 2 residues, 2 models selected > distance #2/H:100A@O #2/A:169@N Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/H PRO 100A O and /A ASN 169 N: 2.681 > select up 27 atoms, 26 bonds, 2 residues, 2 models selected > show sel cartoons > select #2/A:164 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/A:164@O 1 atom, 1 residue, 1 model selected > select add #2/H:100F@OH 2 atoms, 2 residues, 2 models selected > distance #2/A:164@O #2/H:100F@OH Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/A ILE 164 O and /H TYR 100F OH: 2.667 > select #2/A:164@CA 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 2 models selected > show sel cartoons > select #2/A:126 11 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:125B 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/A:125B@O 1 atom, 1 residue, 1 model selected > select add #2/H:32@OH 2 atoms, 2 residues, 2 models selected > distance #2/A:125B@O #2/H:32@OH Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/A SER 125B O and /H TYR 32 OH: 2.433 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 2 models selected > show sel cartoons > select #2/H:96@CG 1 atom, 1 residue, 1 model selected > select add #2/A:128@CG 2 atoms, 2 residues, 1 model selected > distance #2/H:96@CG #2/A:128@CG Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/H LEU 96 CG and /A PRO 128 CG: 4.188 > distance #2/H:96@CG #2/A:128@CG Window position QRect(2388,390 600x300) outside any known screen, using primary screen Distance already exists; modify distance properties with 'distance style' > distance style color #0096ff > distance style color #00fdff > distance style color #797979 > distance style color #00fdff > distance style color #797979 > select clear > distance style color #00fdff > distance style color #797979 > color sel turquoise > select #2/a:125 17 atoms, 16 bonds, 1 residue, 1 model selected > select #2/H:100B@CG 1 atom, 1 residue, 1 model selected > select add #2/A:124@CG1 2 atoms, 2 residues, 1 model selected > distance #2/H:100B@CG #2/A:124@CG1 Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/H LEU 100B CG and /A ILE 124 CG1: 4.851 > color sel turquoise Drag select of 7 residues > select clear > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!2 atoms > select clear > label delete > select clear > select #2/A:125B,128,169,124,167,164 87 atoms, 82 bonds, 6 residues, 1 model selected > color sel byhetero > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > hide #!2 models > show #!3 models > show #!2 models > hide #!2 models Drag select of 369 residues > select up 22587 atoms, 22873 bonds, 1439 residues, 1 model selected > color sel grey > select clear > select #3/B:175 12 atoms, 11 bonds, 1 residue, 1 model selected > select add #3/b:50 26 atoms, 24 bonds, 2 residues, 1 model selected > select up 7487 atoms, 7581 bonds, 477 residues, 1 model selected > select up 7568 atoms, 7666 bonds, 481 residues, 1 model selected > color sel light grey > select clear Drag select of 60 residues > select up 3095 atoms, 3137 bonds, 203 residues, 1 model selected > select up 3576 atoms, 3624 bonds, 234 residues, 1 model selected > hide sel cartoons > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5.cxs"" includeMaps true > select #3/H:32,100B,100C,100D 72 atoms, 72 bonds, 4 residues, 1 model selected > show sel atoms > color sel byhetero > select #3/H:95-100H,30-34 310 atoms, 317 bonds, 19 residues, 1 model selected > show sel cartoons > select #3/B:9125B,169,166,167 43 atoms, 41 bonds, 3 residues, 1 model selected > show sel atoms > color sel byhetero > select #3/H:32,100B,100C,100D 72 atoms, 72 bonds, 4 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol > false intraRes false reveal true retainCurrent true 3 hydrogen bonds found > select #3/B:167 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/H:100D 21 atoms, 21 bonds, 1 residue, 1 model selected > select #3/B:167 11 atoms, 10 bonds, 1 residue, 1 model selected > select #3/H:100D 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #3/B:167 32 atoms, 31 bonds, 2 residues, 1 model selected > select #3/L:32@CE2 1 atom, 1 residue, 1 model selected > select up 21 atoms, 21 bonds, 1 residue, 1 model selected > hide sel atoms > select #3/B:167 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #3/H:100D 32 atoms, 31 bonds, 2 residues, 1 model selected > hide sel cartoons > select #3/B:167@O 1 atom, 1 residue, 1 model selected > select add #3/H:100D@N 2 atoms, 2 residues, 1 model selected > distance #3/B:167@O #3/H:100D@N Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B SER 167 O and /H TYR 100D N: 3.491 > select add #3/B:167@CA 1 atom, 1 bond, 1 residue, 1 model selected > select up 3 atoms, 1 bond, 2 residues, 1 model selected > select up 32 atoms, 31 bonds, 2 residues, 1 model selected > show sel cartoons > select #3/H:100B 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #3/B:169 24 atoms, 22 bonds, 2 residues, 1 model selected > hide sel cartoons > select #3/B:169@N 1 atom, 1 residue, 1 model selected > select add #3/H:100B@O 2 atoms, 2 residues, 1 model selected > distance #3/B:169@N #3/H:100B@O Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B ASN 169 N and /H SER 100B O: 2.530 > select #3/B:169@CB 1 atom, 1 residue, 1 model selected > select add #3/H:100B@CA 2 atoms, 2 residues, 1 model selected > select up 24 atoms, 22 bonds, 2 residues, 1 model selected > show sel cartoons > select #3/B:125B 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > select #3/B:125B@O 1 atom, 1 residue, 1 model selected > select add #3/H:32@OH 2 atoms, 2 residues, 1 model selected > distance #3/B:125B@O #3/H:32@OH Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B SER 125B O and /H TYR 32 OH: 2.529 > select #3/B:125B@CA 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel cartoons > select #3/H:100C@CD1 1 atom, 1 residue, 1 model selected > select add #3/B:166@CG2 2 atoms, 2 residues, 1 model selected > distance #3/H:100C@CD1 #3/B:166@CG2 Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/H LEU 100C CD1 and /B ILE 166 CG2: 3.613 > color sel turquoise > select clear > select H 51907 atoms, 6741 residues, 4 models selected > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!3 atoms > select clear > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > delete label Missing or invalid ""atoms"" argument: invalid atoms specifier > delete labels Missing or invalid ""atoms"" argument: invalid atoms specifier > labels delete Unknown command: labels delete > label delete > select #3/b:78 15 atoms, 14 bonds, 1 residue, 1 model selected > select clear > select #3/H:100C 19 atoms, 18 bonds, 1 residue, 1 model selected > select #3/B:166 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #3/H:100C 38 atoms, 36 bonds, 2 residues, 1 model selected > color sel byhetero > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5_noncovalent.cxs"" includeMaps > true > show #!2 models > hide #!2 models > show #!2 models > show #!1 models > hide #!3 models > show #!3 models > select ::name=""NAG"" 1340 atoms, 1340 bonds, 54 residues, 4 models selected > show sel & #!1-3 atoms > color sel & #!1-3 byhetero > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!1-3 atoms > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5_noncovalent.cxs"" includeMaps > true > show #4 models > hide #4 models > hide #!3 models > hide #!2 models > show #4 models > hide #4 models > show #!3 models > show #4 models > hide #4 models > hide #!3 models > show #!3 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1/H:100G 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!1 atoms > select clear > show #!2 models > hide #!2 models > show #!3 models > show #!2 models > hide #!2 models > hide #!1 models > select #3/H:100G 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!3 atoms > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!1 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > select #1/H:100C 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #1/H:96 38 atoms, 36 bonds, 2 residues, 1 model selected > select add #1/H:95 50 atoms, 47 bonds, 3 residues, 1 model selected > select add #1/H:97 74 atoms, 70 bonds, 4 residues, 1 model selected > select add #1/H:98 89 atoms, 84 bonds, 5 residues, 1 model selected > select add #1/H:99 113 atoms, 109 bonds, 6 residues, 1 model selected > select add #1/H:100 124 atoms, 119 bonds, 7 residues, 1 model selected > select add #1/H:100A 131 atoms, 125 bonds, 8 residues, 1 model selected > select add #1/H:100B 141 atoms, 134 bonds, 9 residues, 1 model selected > select add #1/H:100G 162 atoms, 155 bonds, 10 residues, 1 model selected > select add #1/H:100H 169 atoms, 161 bonds, 11 residues, 1 model selected > select add #1/H:100E 190 atoms, 182 bonds, 12 residues, 1 model selected > select add #1/H:100F 211 atoms, 203 bonds, 13 residues, 1 model selected > select add #1/H:100D 225 atoms, 216 bonds, 14 residues, 1 model selected > transparency 50 selection Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 50 selected Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 50 selected c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency c 50 selected Missing or invalid ""percent"" argument: Expected a number > transparency select 50 c Missing or invalid ""percent"" argument: Expected a number > transparency 50 selection c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 50 select c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 50 selected c Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels', 'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword > transparency 50 target c > transparency 0 target c > transparency sel 50 target c > select clear > show #!2 models > hide #!2 models > select #1/H:95 12 atoms, 11 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/H:100H 7 atoms, 6 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/H:100B 10 atoms, 9 bonds, 1 residue, 1 model selected > select clear > show #!2 models > show #!3 models > hide #!3 models > hide #!2 models > select clear > select add #1/A:144 10 atoms, 9 bonds, 1 pseudobond, 1 residue, 2 models selected > select subtract #1/A:144 1 pseudobond, 2 models selected > select add #1/A:144 10 atoms, 9 bonds, 1 pseudobond, 1 residue, 2 models selected > select subtract #1/A:144 1 pseudobond, 2 models selected > select add #1/A:144 10 atoms, 9 bonds, 1 pseudobond, 1 residue, 2 models selected > color sel turquoise > select clear > select #1/A:144 10 atoms, 9 bonds, 1 residue, 1 model selected > color sel light grey > select clear > save 6G1_Hbond.png supersample 8 transparentBackground true > hide #!1 models > show #!2 models > show #!1 models > select #2/H:95 15 atoms, 14 bonds, 1 residue, 1 model selected > select add #2/H:100G 22 atoms, 20 bonds, 2 residues, 1 model selected > select add #2/H:100H 39 atoms, 36 bonds, 3 residues, 1 model selected > hide sel cartoons > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!1 models > select #2/H:100F 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #2/H:100E 42 atoms, 42 bonds, 2 residues, 1 model selected > select add #2/H:100D 63 atoms, 63 bonds, 3 residues, 1 model selected > select add #2/H:100C 84 atoms, 84 bonds, 4 residues, 1 model selected > select add #2/H:100B 103 atoms, 102 bonds, 5 residues, 1 model selected > select add #2/H:100A 117 atoms, 116 bonds, 6 residues, 1 model selected > select add #2/H:100 124 atoms, 122 bonds, 7 residues, 1 model selected > select add #2/H:99 138 atoms, 135 bonds, 8 residues, 1 model selected > select add #2/H:98 149 atoms, 145 bonds, 9 residues, 1 model selected > select add #2/H:97 159 atoms, 154 bonds, 10 residues, 1 model selected > select add #2/H:96 178 atoms, 172 bonds, 11 residues, 1 model selected > transparency sel 50 target c > select clear > save 20D10_Hbond.png supersample 8 transparentBackground true > hide #!2 models > show #!3 models > show #!2 models > hide #!2 models > select #3/H:95 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #3/H:100H 21 atoms, 19 bonds, 2 residues, 1 model selected > hide sel cartoons > select #3/H:96 14 atoms, 13 bonds, 1 residue, 1 model selected > hide sel cartoons > select #3/H:97 17 atoms, 16 bonds, 1 residue, 1 model selected > select add #3/H:98 28 atoms, 26 bonds, 2 residues, 1 model selected > select add #3/H:99 52 atoms, 49 bonds, 3 residues, 1 model selected > select add #3/H:100 59 atoms, 55 bonds, 4 residues, 1 model selected > select add #3/H:100A 73 atoms, 69 bonds, 5 residues, 1 model selected > select add #3/H:100B 84 atoms, 79 bonds, 6 residues, 1 model selected > select add #3/H:100C 103 atoms, 97 bonds, 7 residues, 1 model selected > select add #3/H:100D 124 atoms, 118 bonds, 8 residues, 1 model selected > select add #3/H:100E 145 atoms, 139 bonds, 9 residues, 1 model selected > select add #3/H:100F 166 atoms, 160 bonds, 10 residues, 1 model selected > select add #3/H:100G 187 atoms, 181 bonds, 11 residues, 1 model selected > show #!2 models > hide #!2 models > show #!1 models > hide #!1 models > hide #!3 models > show #!3 models > transparency sel 50 target c > select clear > save 12G1_Hbond.png supersample 8 transparentBackground true > show #!2 models > hide #!2 models > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_HCDRs_H5_noncovalent.cxs"" includeMaps > true > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > hide #!3 models > show #!3 models > show #!2 models > hide #!2 models > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/FigureMakingChimeraXSessions/Conservation/sequenceCons_sameClade_2024_allGaraziSequences.cxs"" opened ChimeraX session > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/H5_11SequencesAlignment.aln"" Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre Leon/Flu Andre/GaraziH5/RevisionsWard/H5_11SequencesAlignment.aln --- notes | Alignment identifier is H5_11SequencesAlignment.aln Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5_20D10-coot-38_real_space_refined_060.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Showing conservation header (""seq_conservation"" residue attribute) for alignment H5_11SequencesAlignment.aln Opened 10 sequences from H5_11SequencesAlignment.aln > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/H5_12sequences.aln"" Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre Leon/Flu Andre/GaraziH5/RevisionsWard/H5_12sequences.aln --- notes | Alignment identifier is H5_12sequences.aln Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5_20D10-coot-38_real_space_refined_060.pdb chain A to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain B to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain C to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain a to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain b to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain A to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain C to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain B to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain a to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain b to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Showing conservation header (""seq_conservation"" residue attribute) for alignment H5_12sequences.aln Opened 10 sequences from H5_12sequences.aln > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/H5_12sequences.aln"" Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre Leon/Flu Andre/GaraziH5/RevisionsWard/H5_12sequences.aln --- notes | Alignment identifier is H5_12sequences.aln Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5_20D10-coot-38_real_space_refined_060.pdb chain A to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain B to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain C to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain a to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain b to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain A to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain C to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain B to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain a to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain b to A/Jiangsu/NJ210/2023[H5N1]|A/Jiangsu/NJ210/2023[H5N1]|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Showing conservation header (""seq_conservation"" residue attribute) for alignment H5_12sequences.aln Opened 10 sequences from H5_12sequences.aln > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/H5_12sequences.aln"" Summary of feedback from opening /Users/aleon/Scripps Research Dropbox/Andre Leon/Flu Andre/GaraziH5/RevisionsWard/H5_12sequences.aln --- notes | Alignment identifier is H5_12sequences.aln Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_6G1-coot-11_renumbered_real_space_refined_018.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5_20D10-coot-38_real_space_refined_060.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5_20D10-coot-38_real_space_refined_060.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain A to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain C to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain B to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain a to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches Associated H5+12G1_coot-0-coot-32_real_space_refined_036.pdb chain b to A/Jiangsu/NJ210/2023(H5N1)|A/Jiangsu/NJ210/2023(H5N1)|2.3.4.4b|2023-02-10 with 0 mismatches 1 messages similar to the above omitted Showing conservation header (""seq_conservation"" residue attribute) for alignment H5_12sequences.aln Opened 12 sequences from H5_12sequences.aln > select #1/A:125@CB 1 atom, 1 residue, 1 model selected > select up 14 atoms, 14 bonds, 1 residue, 2 models selected > select up 221 atoms, 223 bonds, 12 residues, 2 models selected > select up 4285 atoms, 4343 bonds, 269 residues, 2 models selected > select up 5018 atoms, 5086 bonds, 317 residues, 2 models selected > select up 5045 atoms, 5114 bonds, 318 residues, 2 models selected > select clear > hide #2 models > show #2 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > select add #1 26505 atoms, 26853 bonds, 1688 residues, 1 model selected > select subtract #1 6 models selected Drag select of H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_A SES surface, 143751 of 345860 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_B SES surface, 139576 of 352546 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_C SES surface, 130568 of 351158 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_a SES surface, 122587 of 239464 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_b SES surface, 128984 of 244122 triangles, H5_6G1-coot-11_renumbered_real_space_refined_018.pdb_c SES surface, 143182 of 233634 triangles, 42 atoms, 631 residues, 42 bonds > select up 9829 atoms, 9907 bonds, 634 residues, 7 models selected > select up 18234 atoms, 18443 bonds, 1158 residues, 7 models selected > select up 22931 atoms, 23229 bonds, 1452 residues, 7 models selected > color byattribute seq_conservation sel palette ""dark slate gray:sandy > brown:moccasin:light yellow:white"" key true > key darkslategrey:-4.895 sandybrown:-3.595 moccasin:-2.294 > lightyellow:-0.994 white:0.306 showTool true > ui mousemode right ""color key"" 22931 atoms, 1452 residues, 6 surfaces, atom seq_conservation range -4.89 to 0.306 > key white:0.306 lightyellow:-0.994 moccasin:-2.294 sandybrown:-3.595 > darkslategrey:-4.895 > key colorTreatment distinct > lighting soft > graphics silhouettes false > graphics silhouettes true > select #1/A:240@CG 1 atom, 1 residue, 1 model selected > select clear > key pos 0.683575,0.807168 size 0,0 > select #1-3/H:100A-102 516 atoms, 526 bonds, 32 residues, 3 models selected > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/conservation_H5_12seq_2344bonly.cxs"" > includeMaps true > transparency sel 15 target c > select clear > hide #2 models > show #2 models > hide #!3 models > hide #!1 models > show #!1 models > hide #2 models > show #2 models > hide #2 models > show #2 models > hide #2 models > select #1/H:100A 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #1/H:100C 26 atoms, 24 bonds, 2 residues, 1 model selected > select add #1/H:100B 36 atoms, 33 bonds, 3 residues, 1 model selected > select add #1/H:100D 50 atoms, 46 bonds, 4 residues, 1 model selected > select add #1/H:100E 71 atoms, 67 bonds, 5 residues, 1 model selected > select add #1/H:100F 92 atoms, 88 bonds, 6 residues, 1 model selected > select add #1/H:100G 113 atoms, 109 bonds, 7 residues, 1 model selected > select add #1/H:100H 120 atoms, 115 bonds, 8 residues, 1 model selected > select add #1/H:100I 137 atoms, 131 bonds, 9 residues, 1 model selected > select add #1/H:101 149 atoms, 142 bonds, 10 residues, 1 model selected > select add #1/H:102 165 atoms, 157 bonds, 11 residues, 1 model selected > select clear > show #2 models > show #!3 models > ui tool show ""Side View"" > select #1-3/H:100A-102 516 atoms, 526 bonds, 32 residues, 3 models selected > transparency sel 20 > transparency sel 20 target ac > select clear > select #1-3/H:100A-102 516 atoms, 526 bonds, 32 residues, 3 models selected > transparency sel 40 target ac > transparency sel 50 target ac > select clear > save seqConsTransCDRH3.png supersample 8 tranparentBackground true Expected a keyword > save seqConsTransCDRH3.png supersample 8 transparentBackground true > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/conservation_H5_12seq_2344bonly.cxs"" > hide #!3 models > hide #2 models > show #2 models > hide #!1 models > show #!1 models > hide #2 models > select #1/H:100A 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #1/H:100C 26 atoms, 24 bonds, 2 residues, 1 model selected > select add #1/H:100B 36 atoms, 33 bonds, 3 residues, 1 model selected > select add #1/H:100D 50 atoms, 46 bonds, 4 residues, 1 model selected > select add #1/H:100E 71 atoms, 67 bonds, 5 residues, 1 model selected > select add #1/H:100F 92 atoms, 88 bonds, 6 residues, 1 model selected > select add #1/H:100H 99 atoms, 94 bonds, 7 residues, 1 model selected > select add #1/H:100G 120 atoms, 115 bonds, 8 residues, 1 model selected > select add #1/H:100I 137 atoms, 131 bonds, 9 residues, 1 model selected > select add #1/H:101 149 atoms, 142 bonds, 10 residues, 1 model selected > select add #1/H:102 165 atoms, 157 bonds, 11 residues, 1 model selected > hide sel cartoons > hide sel atoms > show #2 models > save seqConsTransCDRH3_clone1Only.png supersample 8 transparentBackground > true > select #1-3/H:100A-102 516 atoms, 526 bonds, 32 residues, 3 models selected > transparency sel 0 target ac > select clear > save seqConsNotTransCDRH3_clone1Only.png supersample 8 transparentBackground > true > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/conservation_H5_12seq_2344bonly.cxs"" > ui mousemode right translate opened ChimeraX session > select #1-3/H:100A-102 516 atoms, 526 bonds, 32 residues, 3 models selected > transparency sel 0 target ac > select clear > save seqConsNotTransCDRH3_AllClones.png supersample 8 transparentBackground > true > open ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/overlays_Ribbon_slab_noH_noSCs.cxs"" opened ChimeraX session > lighting soft > hide #!3 models > hide #!2 models > show #!2 models > show #!3 models > hide #!1-3 surfaces > hide #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!2 models > show #!1 models > preset cartoons/nucleotides licorice/ovals Using preset: Cartoons/Nucleotides / Licorice/Ovals Changed 0 atom styles Preset expands to these ChimeraX commands: show nucleic hide protein|solvent|H surf hide style (protein|nucleic|solvent) & @@draw_mode=0 stick ~worm cartoon cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20 cartoon style ~(nucleic|strand) x round cartoon style (nucleic|strand) x rect cartoon style protein modeh default arrows f x round width 1 thick 1 cartoon style nucleic x round width 1.6 thick 1.6 nucleotides tube/slab shape ellipsoid > hide #!2 models > hide #!1 models Drag select of 500 residues > select up 22587 atoms, 22873 bonds, 1439 residues, 1 model selected > select up 22845 atoms, 23143 bonds, 1451 residues, 1 model selected > hide sel cartoons > show #!2 models > show #!1 models > hide #!1 models Drag select of 69 atoms, 466 residues, 70 bonds > select up 7568 atoms, 7632 bonds, 471 residues, 7 models selected > select up 7633 atoms, 7697 bonds, 471 residues, 7 models selected > select up 12311 atoms, 12424 bonds, 771 residues, 7 models selected > select up 22973 atoms, 23273 bonds, 1455 residues, 7 models selected > hide sel cartoons > hide #!2 models > show #!1 models > show #!2 models > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs"" includeMaps true > select clear Drag select of 286 residues > select up 9799 atoms, 9933 bonds, 645 residues, 3 models selected > select up 10699 atoms, 10845 bonds, 704 residues, 3 models selected > select clear > hide #!2 models > hide #!3 models > show #!2 models > hide #!1 models > show #!1 models > hide #!1 models > show #!3 models > hide #!2 models > show #!2 models > show #!1 models > hide #!1 models > select add #2 26522 atoms, 26870 bonds, 1689 residues, 1 model selected > show sel cartoons > select add #3 52943 atoms, 53637 bonds, 3374 residues, 8 models selected > select subtract #2 26421 atoms, 26767 bonds, 1685 residues, 7 models selected > hide #!2 models > show sel cartoons > select clear Drag select of 607 residues > select up 22587 atoms, 22873 bonds, 1439 residues, 1 model selected > select up 22845 atoms, 23143 bonds, 1451 residues, 1 model selected > color sel grey > select clear > select #3/b:59 17 atoms, 16 bonds, 1 residue, 1 model selected > select add #3/B:239 31 atoms, 30 bonds, 2 residues, 1 model selected > select up 7487 atoms, 7581 bonds, 477 residues, 1 model selected > select up 7568 atoms, 7666 bonds, 481 residues, 1 model selected > color sel light grey > select clear > show #!2 models > show #!1 models > hide #!3 models > hide #!1 models > select #2/L:56,49,53,27E,28 77 atoms, 75 bonds, 5 residues, 1 model selected > show sel atoms > select clear Drag select of 70 residues > select up 3204 atoms, 3248 bonds, 211 residues, 1 model selected > select up 3549 atoms, 3597 bonds, 234 residues, 1 model selected > hide sel cartoons > select #2/L:56,49,53,27E,28 77 atoms, 75 bonds, 5 residues, 1 model selected > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol > false intraRes false reveal true retainCurrent true 5 hydrogen bonds found > select #2/L:49-56,27D-29 175 atoms, 176 bonds, 12 residues, 1 model selected > show sel cartoons > color sel byhetero > select #2/A:163 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #2/B:220 38 atoms, 36 bonds, 2 residues, 2 models selected > select subtract #2/B:220 14 atoms, 13 bonds, 1 residue, 3 models selected > select add #2/B:227 38 atoms, 36 bonds, 2 residues, 2 models selected > color sel byhetero > select clear > select #2/A:162 14 atoms, 14 bonds, 1 residue, 1 model selected > show sel atoms > color sel byhetero > select clear > select #2/L:27D 17 atoms, 17 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/L:56@CG 1 atom, 1 residue, 1 model selected > select add #2/A:162@CG 2 atoms, 2 residues, 1 model selected > ui tool show Distances > distance #2/L:56@CG #2/A:162@CG Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/L PRO 56 CG and /A PRO 162 CG: 3.693 > select #2/L:53@OD1 1 atom, 1 residue, 1 model selected > select add #2/A:163@OG1 2 atoms, 2 residues, 1 model selected > distance #2/L:53@OD1 #2/A:163@OG1 Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/L ASP 53 OD1 and /A THR 163 OG1: 3.224 > select #2/A:163 14 atoms, 13 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/A:163@O 1 atom, 1 residue, 1 model selected > select add #2/L:49@OH 2 atoms, 2 residues, 2 models selected > distance #2/A:163@O #2/L:49@OH Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/A THR 163 O and /L TYR 49 OH: 2.735 > select #2/A:163@C 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel cartoons > select #2/L:27E 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/B:227@NH2 1 atom, 1 residue, 1 model selected > select add #2/L:27E@O 2 atoms, 2 residues, 2 models selected > distance #2/B:227@NH2 #2/L:27E@O Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/B ARG 227 NH2 and /L SER 27E O: 3.130 > select #2/B:227@NH1 1 atom, 1 residue, 1 model selected > select add #2/L:27E@O 2 atoms, 2 residues, 2 models selected > distance #2/B:227@NH1 #2/L:27E@O Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/B ARG 227 NH1 and /L SER 27E O: 3.344 > select #2/L:27E@CB 1 atom, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel cartoons > select #2/L:28 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/B:227@NH1 1 atom, 1 residue, 1 model selected > select add #2/L:28@O 2 atoms, 2 residues, 2 models selected > distance #2/B:227@NH1 #2/L:28@O Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/B ARG 227 NH1 and /L ILE 28 O: 3.083 > select #2/L:28@CB 1 atom, 1 residue, 1 model selected > select up 19 atoms, 18 bonds, 1 residue, 1 model selected > show sel cartoons > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!2 atoms > label delete > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs"" includeMaps true > hide #!2 models > show #!1 models > select #1/L:49,30,28,53,67,28 85 atoms, 83 bonds, 5 residues, 1 model selected > show sel atoms > color sel byhetero > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol > false intraRes false reveal true retainCurrent true 6 hydrogen bonds found > hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol > false intraRes false reveal true retainCurrent true 6 hydrogen bonds found Drag select of 143 residues > select up 3539 atoms, 3589 bonds, 234 residues, 1 model selected > select up 3574 atoms, 3624 bonds, 236 residues, 1 model selected > hide sel cartoons > select #1/L:28-31,66-68,49-53 157 atoms, 157 bonds, 12 residues, 1 model selected > show sel cartoons > select clear > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > select #1/L:27-31,66-68,49-53 251 atoms, 252 bonds, 18 residues, 1 model selected > show sel cartoons > select #1/L:27A 11 atoms, 10 bonds, 1 residue, 1 model selected > select up 1674 atoms, 1696 bonds, 111 residues, 1 model selected > hide sel cartoons > select #1/L:27E-31,66-68,49-53 168 atoms, 168 bonds, 13 residues, 1 model selected > show sel cartoons > select clear > select #1/A:165 22 atoms, 21 bonds, 1 residue, 1 model selected > select add #1/A:169 35 atoms, 33 bonds, 2 residues, 2 models selected > select add #1/A:246 50 atoms, 47 bonds, 3 residues, 2 models selected > select add #1/B:187 64 atoms, 60 bonds, 4 residues, 2 models selected > color sel byhetero > select clear > select #1/L:53@OH 1 atom, 1 residue, 1 model selected > select add #1/A:246@OE2 2 atoms, 2 residues, 1 model selected > distance #1/L:53@OH #1/A:246@OE2 Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/L TYR 53 OH and /A GLU 246 OE2: 2.663 > select #1/B:187@ND2 1 atom, 1 residue, 1 model selected > select add #1/L:67@OG 2 atoms, 2 residues, 2 models selected > distance #1/B:187@ND2 #1/L:67@OG Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/B ASN 187 ND2 and /L SER 67 OG: 3.323 > select #1/A:165@NZ 1 atom, 1 residue, 1 model selected > select add #1/L:30@OG 2 atoms, 2 residues, 2 models selected > distance #1/A:165@NZ #1/L:30@OG Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/A LYS 165 NZ and /L SER 30 OG: 2.526 > select #1/A:163 14 atoms, 13 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/A:163@O 1 atom, 1 residue, 1 model selected > select add #1/L:49@OH 2 atoms, 2 residues, 2 models selected > distance #1/A:163@O #1/L:49@OH Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/A THR 163 O and /L TYR 49 OH: 2.672 > select clear > select #1/A:163@CA 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel cartoons > select #1/A:169@ND2 1 atom, 1 residue, 1 model selected > select add #1/L:28@OH 2 atoms, 2 residues, 2 models selected > distance #1/A:169@ND2 #1/L:28@OH Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/A ASN 169 ND2 and /L TYR 28 OH: 2.563 > select #1/B:227 24 atoms, 23 bonds, 1 residue, 1 model selected > show sel atoms > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol > false intraRes false reveal true retainCurrent true 0 hydrogen bonds found > color sel byhetero > select #1/L:28 21 atoms, 21 bonds, 1 residue, 1 model selected > hide sel cartoons > select #1/B:227@CZ 1 atom, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 1 residue, 2 models selected > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false angleSlop 100.0 intraMol > false intraRes false reveal true retainCurrent true 0 hydrogen bonds found > hbonds sel color #797979 dashes 6 interModel false distSlop 0.5 angleSlop > 100.0 intraMol false intraRes false reveal true retainCurrent true 0 hydrogen bonds found > select #1/B:227@CD 1 atom, 1 residue, 1 model selected > select up 24 atoms, 23 bonds, 1 residue, 2 models selected > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false distSlop 0.5 angleSlop > 200.0 intraMol false intraRes false reveal true retainCurrent true 0 hydrogen bonds found > hbonds sel color #797979 dashes 6 interModel false distSlop 0.6 angleSlop > 100.0 intraMol false intraRes false reveal true retainCurrent true 0 hydrogen bonds found > select #1/L:28@H 1 atom, 1 residue, 1 model selected > select add #1/B:227@NH2 2 atoms, 2 residues, 1 model selected > select #1/L:28@N 1 atom, 1 residue, 1 model selected > select add #1/B:227@NH2 2 atoms, 2 residues, 1 model selected > distance #1/L:28@N #1/B:227@NH2 Distance between H5_6G1-coot-11_renumbered_real_space_refined_018.pdb #1/L TYR 28 N and /B ARG 227 NH2: 3.144 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 21 atoms, 21 bonds, 1 residue, 1 model selected > show sel cartoons > select clear > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!1 atoms > select clear > delete label Missing or invalid ""atoms"" argument: invalid atoms specifier > delete labels Missing or invalid ""atoms"" argument: invalid atoms specifier > label delete > select clear > show #!3 models > hide #!1 models > select #3/L:52,53,30,28,56,49,28,27E 108 atoms, 106 bonds, 7 residues, 1 model selected > show sel atoms > color sel byhetero > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs"" includeMaps true > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false distSlop 0.6 angleSlop > 100.0 intraMol false intraRes false reveal true retainCurrent true 9 hydrogen bonds found > select #3/B:129 14 atoms, 13 bonds, 1 residue, 1 model selected > select add #3/B:165 36 atoms, 34 bonds, 2 residues, 1 model selected > select add #3/B:167 47 atoms, 44 bonds, 3 residues, 1 model selected > select add #3/C:222 64 atoms, 60 bonds, 4 residues, 1 model selected > select add #3/B:170 78 atoms, 73 bonds, 5 residues, 1 model selected > select subtract #3/B:170 64 atoms, 60 bonds, 4 residues, 1 model selected > select add #3/B:169 77 atoms, 72 bonds, 5 residues, 1 model selected > color sel byhetero > select clear Drag select of 101 residues > select up 3303 atoms, 3349 bonds, 217 residues, 1 model selected > select up 3576 atoms, 3624 bonds, 234 residues, 1 model selected > hide sel cartoons > select clear > select #3/L:28@OH 1 atom, 1 residue, 1 model selected > select add #3/B:169@ND2 2 atoms, 2 residues, 1 model selected > distance #3/L:28@OH #3/B:169@ND2 Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/L TYR 28 OH and /B ASN 169 ND2: 2.558 > select #3/L:27E@O 1 atom, 1 residue, 1 model selected > select add #3/C:222@NE2 2 atoms, 2 residues, 1 model selected > distance #3/L:27E@O #3/C:222@NE2 Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/L SER 27E O and /C GLN 222 NE2: 3.268 > select #3/L:30@OH 1 atom, 1 residue, 1 model selected > select add #3/B:167@OG 2 atoms, 2 residues, 1 model selected > distance #3/L:30@OH #3/B:167@OG Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/L TYR 30 OH and /B SER 167 OG: 2.289 > select #3/L:56@OG 1 atom, 1 residue, 1 model selected > select add #3/B:129@OD1 2 atoms, 2 residues, 1 model selected > distance #3/L:56@OG #3/B:129@OD1 Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/L SER 56 OG and /B ASN 129 OD1: 2.905 > select #3/B:165@NZ 1 atom, 1 residue, 1 model selected > select add #3/L:52@OG 2 atoms, 2 residues, 1 model selected > distance #3/B:165@NZ #3/L:52@OG Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B LYS 165 NZ and /L SER 52 OG: 3.058 > select #3/B:165@NZ 1 atom, 1 residue, 1 model selected > select add #3/L:53@OD2 2 atoms, 2 residues, 1 model selected > distance #3/B:165@NZ #3/L:53@OD2 Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B LYS 165 NZ and /L ASP 53 OD2: 3.296 > select #3/B:163 14 atoms, 13 bonds, 1 residue, 1 model selected > hide sel cartoons > select #3/B:163@O 1 atom, 1 residue, 1 model selected > select add #3/L:49@OH 2 atoms, 2 residues, 1 model selected > distance #3/B:163@O #3/L:49@OH Distance between H5+12G1_coot-0-coot-32_real_space_refined_036.pdb #3/B THR 163 O and /L TYR 49 OH: 3.479 > select #3/B:163@C 1 atom, 1 residue, 1 model selected > select up 14 atoms, 13 bonds, 1 residue, 1 model selected > select up 4905 atoms, 4970 bonds, 312 residues, 1 model selected > select down 14 atoms, 13 bonds, 1 residue, 1 model selected > show sel cartoons > select #3/L:27E-31,48-56 213 atoms, 214 bonds, 14 residues, 1 model selected > show sel cartoons > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!3 atoms > label delete > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs"" includeMaps true > select clear > show #!2 models > show #!1 models > hide #!1 models > hide #!2 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > show #!2 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!3 models > hide #!3 models > show #!2 models > select clear > delete sel > ~distance #2/B:227@NH2 #2/L:27E@O > ~distance #2/B:227@NH1 #2/L:27E@O > select #2/B:227@NH2 1 atom, 1 residue, 1 model selected > ui tool show H-Bonds > hbonds sel color #797979 dashes 6 interModel false distSlop 0.6 angleSlop > 100.0 intraMol false intraRes false reveal true retainCurrent true 2 hydrogen bonds found > select #2/L:27E 11 atoms, 10 bonds, 1 residue, 1 model selected > hide sel cartoons > select #2/L:27E@O 1 atom, 1 residue, 1 model selected > select add #2/B:227@NH2 2 atoms, 1 pseudobond, 2 residues, 2 models selected > distance #2/L:27E@O #2/B:227@NH2 Distance between H5_20D10-coot-38_real_space_refined_060.pdb #2/L SER 27E O and /B ARG 227 NH2: 3.130 > select up 2 atoms, 1 bond, 1 residue, 1 model selected > select up 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel cartoons > select H 51907 atoms, 6741 residues, 4 models selected > hide sel & #!2 atoms > select clear > select #2/L:27D@C 1 atom, 1 residue, 1 model selected > select up 17 atoms, 17 bonds, 1 residue, 1 model selected > hide sel atoms > label delete > select clear > color sel turquoise > select clear > hide #!2 models > show #!3 models > show #!2 models > hide #!3 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > select #2/L:27E 11 atoms, 10 bonds, 1 residue, 1 model selected > transparency sel 50 target c > select clear > show #!3 models > show #!1 models > hide #!2 models > hide #!3 models > select #1/L:27E 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/L:49 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #1/L:50 40 atoms, 39 bonds, 2 residues, 1 model selected > select #1/L:27E 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #1/L:49 32 atoms, 31 bonds, 2 residues, 1 model selected > select add #1/L:50 51 atoms, 49 bonds, 3 residues, 1 model selected > transparency sel 50 target c > select clear > select #1/L:27E 11 atoms, 10 bonds, 1 residue, 1 model selected > select add #1/L:31 25 atoms, 23 bonds, 2 residues, 1 model selected > hide sel cartoons > show #!2 models > hide #!1 models > hide #!2 models > show #!3 models > select #3/L:48 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel cartoons > select #3/L:49 21 atoms, 21 bonds, 1 residue, 1 model selected > select #3/L:53 12 atoms, 11 bonds, 1 residue, 1 model selected > select #3/L:49 21 atoms, 21 bonds, 1 residue, 1 model selected > select #3/L:50 19 atoms, 18 bonds, 1 residue, 1 model selected > select add #3/L:49 40 atoms, 39 bonds, 2 residues, 1 model selected > select add #3/L:51 47 atoms, 45 bonds, 3 residues, 1 model selected > transparency sel 50 target c > select clear > select #3/L:31 19 atoms, 18 bonds, 1 residue, 1 model selected > hide sel cartoons > select clear > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs"" includeMaps true > show #!2 models > hide #!3 models > select #2/L:49 21 atoms, 21 bonds, 1 residue, 1 model selected > select add #2/L:50 40 atoms, 39 bonds, 2 residues, 1 model selected > transparency sel 50 target c > select clear > show #!1 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!3 models > show #!2 models > hide #!3 models > show #!3 models > hide #!1 models > show #!1 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!3 models > show #!1 models > hide #!1 models > show #!1 models > hide #!3 models > hide #!2 models > show #!2 models > hide #!1 models > show #!1 models > show #!3 models > hide #!2 models > hide #!3 models > show #!2 models > hide #!1 models > show #!1 models > show #!3 models > hide #!2 models > hide #!1 models > show #!1 models > hide #!3 models > show #!3 models > hide #!3 models > hide #!1 models > show #!2 models > show #!1 models > show #!3 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > hide #!2 models > show #4 models > hide #4 models > hide #!3 models > show #!2 models > hide #!2 models > show #!2 models > hide #!2 models > show #!2 models > show #!3 models > hide #!2 models > show #!2 models > hide #!3 models > hide #!2 models > hide #!1 models > show #!1 models > show #!2 models > show #!3 models > save ""/Users/aleon/Scripps Research Dropbox/Andre Leon/Flu > Andre/GaraziH5/RevisionsWard/Updated_CDRLs_H5.cxs"" includeMaps true > hide #!3 models > hide #!2 models > save 6G1_CDRL_H5.png supersample 8 transparentBackground true > hide #!1 models > show #!1 models > show #!2 models > hide #!1 models > save 20D10_CDRL_H5.png supersample 8 transparentBackground true > show #!3 models > hide #!2 models > save 12G1_CDRL_H5.png supersample 8 transparentBackground true ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 Max OpenGL vendor: Apple Python: 3.11.4 Locale: UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Pro Model Identifier: MacBookPro18,2 Model Number: Z14W00106LL/A Chip: Apple M1 Max Total Number of Cores: 10 (8 performance and 2 efficiency) Memory: 32 GB System Firmware Version: 10151.140.19 OS Loader Version: 10151.140.19 Software: System Software Overview: System Version: macOS 14.6.1 (23G93) Kernel Version: Darwin 23.6.0 Time since boot: 77 days, 22 hours, 9 minutes Graphics/Displays: Apple M1 Max: Chipset Model: Apple M1 Max Type: GPU Bus: Built-In Total Number of Cores: 24 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: Yes Connection Type: Internal LG UltraFine: Resolution: 4096 x 2304 UI Looks like: 2048 x 1152 @ 60.00Hz Mirror: Off Online: Yes Rotation: Supported Automatically Adjust Brightness: No Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX