id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15999 Crash in garbage collection chimerax-bug-report@… Eric Pettersen "{{{ The following bug report has been submitted: Platform: macOS-14.5-x86_64-i386-64bit ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC) Description Last time you used ChimeraX it crashed. Please describe steps that led to the crash here. Fatal Python error: Segmentation fault Thread 0x0000000321b61000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000320b5e000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031fb5b000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 502 in _wait_for_updates File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031eb58000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031db55000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031cb52000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031bb4f000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x000000031ab4c000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000319b49000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000318b46000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Thread 0x0000000317b43000 (most recent call first): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap Current thread 0x000000020466b240 (most recent call first): Garbage-collecting File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py"", line 161 in __iter__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py"", line 907 in atomspec_atoms File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 627 in _add_model_parts File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 476 in _check File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 490 in _check File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 470 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 612 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 455 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1004 in find_matches File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1001 in evaluate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/atomspec.py"", line 1091 in evaluate File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 36 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/args.py"", line 71 in parse File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2499 in _parse_arg File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2640 in _process_positional_arguments File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2864 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 3468 in __call__ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py"", line 2929 in run File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 319 in execute File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py"", line 146 in keyPressEvent File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py"", line 275 in event_loop File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 918 in init File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py"", line 1069 in File """", line 88 in _run_code File """", line 198 in _run_module_as_main Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.pdb_lib._load_libs, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 56) {""app_name"":""ChimeraX"",""timestamp"":""2024-09-23 14:53:56.00 -0500"",""app_version"":""1.7.1"",""slice_uuid"":""194a3167-3db5-3029-8d22-1d742b826bb9"",""build_version"":""1.7.1.0"",""platform"":1,""bundleID"":""edu.ucsf.cgl.ChimeraX"",""share_with_app_devs"":0,""is_first_party"":0,""bug_type"":""309"",""os_version"":""macOS 14.5 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University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_FL/fold_2024_08_23_12_59_model_0.cif Chain information for fold_2024_08_23_12_59_model_0.cif #1 --- Chain | Description A B C | . > set bgColor white > graphics silhouettes true > open 7fbi Summary of feedback from opening 7fbi fetched from pdb --- note | Fetching compressed mmCIF 7fbi from http://files.rcsb.org/download/7fbi.cif 7fbi title: Cryo-EM structure of EBV gB in complex with nAbs 3A3 and 3A5 [more info...] Chain information for 7fbi #2 --- Chain | Description | UniProt A | Envelope glycoprotein B | R4R670_EBVG 22-674 H | 3A3 heavy chain | L | 3A3 light chain | M | 3A5 light chain | N | 3A5 heavy chain | > select add #2 7777 atoms, 7940 bonds, 3 pseudobonds, 1005 residues, 2 models selected > show sel cartoons > hide sel atoms > mmaker #2 to #! > matchmaker #2 to #! Invalid ""to"" argument: invalid atoms specifier > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_08_23_12_59_model_0.cif, chain A (#1) with 7fbi, chain A (#2), sequence alignment score = 1187.8 RMSD between 194 pruned atom pairs is 1.238 angstroms; (across all 548 pairs: 4.367) > ui mousemode right select > select clear > select #2/A:160 8 atoms, 7 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A Alignment identifier is 2/A > select clear > select #2/A:538 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/A:538-539 19 atoms, 18 bonds, 2 residues, 1 model selected > select #2/A:112 10 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:112-113 21 atoms, 21 bonds, 2 residues, 1 model selected > select #1/A:129 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:128 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:129 7 atoms, 6 bonds, 1 residue, 1 model selected > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/HHV6A/AF3/HHV6A_gB_GS_FL/fold_2024_09_02_11_52_model_0.cif Chain information for fold_2024_09_02_11_52_model_0.cif #3 --- Chain | Description A B C | . > select down 7 atoms, 6 bonds, 1 residue, 1 model selected > select ~sel & ##selected 19823 atoms, 20247 bonds, 2534 residues, 1 model selected > select ~sel & ##selected 7 atoms, 6 bonds, 1 residue, 1 model selected > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_08_23_12_59_model_0.cif, chain A (#1) with fold_2024_09_02_11_52_model_0.cif, chain A (#3), sequence alignment score = 1481.2 RMSD between 357 pruned atom pairs is 1.205 angstroms; (across all 770 pairs: 19.068) > hide #1 models > select add #1 19830 atoms, 20253 bonds, 2535 residues, 1 model selected > color #2 #919191ff > select #2/A:112 10 atoms, 10 bonds, 1 residue, 1 model selected > select #2/A:112-113 21 atoms, 21 bonds, 2 residues, 1 model selected > show #1 models > hide #3 models > select #1/A:209 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:213 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:212 4 atoms, 3 bonds, 1 residue, 1 model selected > show #3 models > select #3/A:103 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/C:154 9 atoms, 8 bonds, 1 residue, 1 model selected > select #3/A:185 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:187 14 atoms, 15 bonds, 1 residue, 1 model selected > select #3/A:188 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:185 7 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:187 14 atoms, 15 bonds, 1 residue, 1 model selected > hide #3 models > select add #3 19677 atoms, 20088 bonds, 2490 residues, 1 model selected > hide #!2 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C Alignment identifier is 1 > select #1/A-C:52-56 99 atoms, 96 bonds, 15 residues, 1 model selected > select #1/A-C:1-56 1173 atoms, 1197 bonds, 168 residues, 1 model selected > select #1/A-C:1-56 1173 atoms, 1197 bonds, 168 residues, 1 model selected > select #1/A-C:1-56 1173 atoms, 1197 bonds, 168 residues, 1 model selected > select #1/A-C:57 21 atoms, 21 bonds, 3 residues, 1 model selected > select #1/A-C:1-57 1194 atoms, 1221 bonds, 171 residues, 1 model selected > open 5ㅊㅌㄹ Traceback (most recent call last): File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/cmd_line/tool.py"", line 319, in execute cmd.run(cmd_text) File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 131, in cmd_open models = Command(session, registry=registry).run(provider_cmd_text, log=log)[0] ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/commands/cli.py"", line 2908, in run result = ci.function(session, **kw_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 166, in provider_open models, status = collated_open(session, database_name, ident, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 513, in collated_open return remember_data_format() ^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/open_command/cmd.py"", line 484, in remember_data_format models, status = func(*func_args, **func_kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/mmcif/__init__.py"", line 108, in fetch return fetcher(session, ident, ignore_cache=ignore_cache, **kw) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""src/mmcif.pyx"", line 426, in chimerax.mmcif.mmcif.fetch_mmcif File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/fetch.py"", line 99, in fetch_file retrieve_url(url, filename, uncompress=uncompress, transmit_compressed=transmit_compressed, File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site- packages/chimerax/core/fetch.py"", line 192, in retrieve_url with urlopen(request, timeout=timeout, context=ssl_context) as response: ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 216, in urlopen return opener.open(url, data, timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 519, in open response = self._open(req, data) ^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 536, in _open result = self._call_chain(self.handle_open, protocol, protocol + ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 496, in _call_chain result = func(*args) ^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 1377, in http_open return self.do_open(http.client.HTTPConnection, req) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py"", line 1348, in do_open h.request(req.get_method(), req.selector, req.data, headers, File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1282, in request self._send_request(method, url, body, headers, encode_chunked) File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1293, in _send_request self.putrequest(method, url, **skips) File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1131, in putrequest self._output(self._encode_request(request)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1211, in _encode_request return request.encode('ascii') ^^^^^^^^^^^^^^^^^^^^^^^ UnicodeEncodeError: 'ascii' codec can't encode characters in position 15-17: ordinal not in range(128) UnicodeEncodeError: 'ascii' codec can't encode characters in position 15-17: ordinal not in range(128) File ""/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py"", line 1211, in _encode_request return request.encode('ascii') ^^^^^^^^^^^^^^^^^^^^^^^ See log for complete Python traceback. > open 5cxf 5cxf title: Crystal structure of the extracellular domain of glycoprotein B from Human Cytomegalovirus [more info...] Chain information for 5cxf #4 --- Chain | Description | UniProt A B C | Envelope glycoprotein B | GB_HCMVA 78-706 Non-standard residues in 5cxf #4 --- BMA — beta-D-mannopyranose (beta-D-mannose; D-mannose; mannose) CA — calcium ion MAN — alpha-D-mannopyranose (alpha-D-mannose; D-mannose; mannose) NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) > mmaker #4 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_08_23_12_59_model_0.cif, chain A (#1) with 5cxf, chain B (#4), sequence alignment score = 1185.8 RMSD between 314 pruned atom pairs is 1.313 angstroms; (across all 565 pairs: 3.066) > select clear > select #4/C:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/C:156 10 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:157 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:156 10 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:157 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:156 10 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:157 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select #4/C:156 10 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:157 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:156 10 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select #4/C:157 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:156 10 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:157 11 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:156 10 atoms, 10 bonds, 1 residue, 1 model selected > select #4/C:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select #4/C:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/C:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/C:238 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/C:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select clear > select #4/C:238 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/C:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/C:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/C:241 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/C:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/C:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/C:238 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/C:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/C:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/C:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/C:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/C:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/C:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/C:239 7 atoms, 6 bonds, 1 residue, 1 model selected > show #3 models > hide #!4 models > select add #4 14373 atoms, 14732 bonds, 12 pseudobonds, 1749 residues, 3 models selected > select #3/A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:187 14 atoms, 15 bonds, 1 residue, 1 model selected > select #3/A:103 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:102 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:103 4 atoms, 3 bonds, 1 residue, 1 model selected > select #3/A:102 7 atoms, 6 bonds, 1 residue, 1 model selected > select #3/A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:187 14 atoms, 15 bonds, 1 residue, 1 model selected > select #3/A:186 8 atoms, 7 bonds, 1 residue, 1 model selected > select #3/A:187 14 atoms, 15 bonds, 1 residue, 1 model selected > select #1/A:129 7 atoms, 6 bonds, 1 residue, 1 model selected > show #!2 models > hide #3 models > select #1/A:130 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/A:131 6 atoms, 5 bonds, 1 residue, 1 model selected > select #1/A:211 7 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:212 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:213 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > select #1/A:212 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/A:213 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:214 12 atoms, 12 bonds, 1 residue, 1 model selected > show #!4 models > select #4/B:242 10 atoms, 10 bonds, 1 residue, 1 model selected > select #1/A:213 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #1 models > hide #!2 models > show #1 models > select add #1 19830 atoms, 20253 bonds, 2535 residues, 1 model selected > color #4 #d4fb79ff > select clear > select #1/A:213 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:214 12 atoms, 12 bonds, 1 residue, 1 model selected > select #1/A:213 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:214 12 atoms, 12 bonds, 1 residue, 1 model selected > select #4/B:242 10 atoms, 10 bonds, 1 residue, 1 model selected > select #4/B:241 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:241 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/B:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/B:241 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/A:213 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/A:214 12 atoms, 12 bonds, 1 residue, 1 model selected > select #4/B:241 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select #4/B:243 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select #4/B:241 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select clear > select #4/B:241 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #4/B:239 7 atoms, 6 bonds, 1 residue, 1 model selected > select #4/B:238 6 atoms, 5 bonds, 1 residue, 1 model selected > select #4/B:240 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/A:701 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > select #4/B:241 7 atoms, 6 bonds, 1 residue, 1 model selected > open 5c6t 5c6t title: Crystal structure of HCMV glycoprotein B in complex with 1G2 Fab [more info...] Chain information for 5c6t #5 --- Chain | Description | UniProt A | Envelope glycoprotein B | GB_HCMVT 87-698 H | 1G2 Fab heavy chain | L | 1G2 Fab light chain | Non-standard residues in 5c6t #5 --- MG — magnesium ion NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 5c6t mmCIF Assemblies --- 1| author_and_software_defined_assembly > hide #!4 models > select add #4 14373 atoms, 14732 bonds, 12 pseudobonds, 1749 residues, 3 models selected > mmaker $5 to $1 > matchmaker $5 to $1 Missing or invalid ""matchAtoms"" argument: invalid atoms specifier > mmaker #5 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_08_23_12_59_model_0.cif, chain A (#1) with 5c6t, chain A (#5), sequence alignment score = 1048.8 RMSD between 231 pruned atom pairs is 1.238 angstroms; (across all 557 pairs: 7.840) > select #5/A:242 7 atoms, 6 bonds, 1 residue, 1 model selected > select #1/C:696 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:241 8 atoms, 7 bonds, 1 residue, 1 model selected > select #5/A:240 8 atoms, 7 bonds, 1 residue, 1 model selected > select clear > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_FL/fold_2024_08_23_12_59_model_0.cif Chain information for fold_2024_08_23_12_59_model_0.cif #6 --- Chain | Description A B C | . > hide #!5 models > hide #6 models > ui tool show ""Show Sequence Viewer"" > sequence chain #1/A #1/B #1/C #6/A #6/B #6/C Alignment identifier is 1 > select #1/A-C:1 #6/A-C:1 48 atoms, 42 bonds, 6 residues, 2 models selected > select #1/A-C:1-477 #6/A-C:1-477 22110 atoms, 22662 bonds, 2862 residues, 2 models selected . [ID: 1] region 6 chains [1-477] RMSD: 0.000 > select clear > select #1/A-C:1-2 #6/A-C:1-2 90 atoms, 84 bonds, 12 residues, 2 models selected > select #1/A-C #6/A-C 39660 atoms, 40506 bonds, 5070 residues, 2 models selected . [ID: 1] region 6 chains [1-845] RMSD: 0.000 > select clear > select #1/C:680 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:674 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/C:674 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:680 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:682 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:683 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:684 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #1/C:680 16 atoms, 14 bonds, 2 residues, 1 model selected > select #1/C:672 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/C:670 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select #1/C:671 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:672 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/C:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #1/C:674 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:675 11 atoms, 10 bonds, 1 residue, 1 model selected > select #1/C:676 9 atoms, 8 bonds, 1 residue, 1 model selected > select #1/C:677 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:678 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:679 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:680 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:670 11 atoms, 10 bonds, 1 residue, 1 model selected > select clear > select #1/C:671 8 atoms, 7 bonds, 1 residue, 1 model selected > select #1/C:672 5 atoms, 4 bonds, 1 residue, 1 model selected > select #1/C:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select clear > show #6 models > show #3 models > hide #6 models > hide #3 models > show #3 models > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_ECD_FD/fold_2024_08_23_17_18_model_0.cif Chain information for fold_2024_08_23_17_18_model_0.cif #7 --- Chain | Description A B C | . > hide #3 models > hide #1 models > select #7/C:640 12 atoms, 12 bonds, 1 residue, 1 model selected > show sel atoms > select #7/C:644 11 atoms, 10 bonds, 1 residue, 1 model selected > show sel atoms > select #7/B:240 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #7/B:241 12 atoms, 10 bonds, 2 residues, 1 model selected > show sel atoms > select #7/C:654 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #7/C:653 16 atoms, 14 bonds, 2 residues, 1 model selected > show sel atoms > select #7/B:241 4 atoms, 3 bonds, 1 residue, 1 model selected > show sel atoms > select #7/C:640 12 atoms, 12 bonds, 1 residue, 1 model selected > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_FL/fold_2024_08_23_12_59_model_0.cif Chain information for fold_2024_08_23_12_59_model_0.cif #8 --- Chain | Description A B C | . > hide #8 models > hide #7 models > show #8 models > select #8/B:685 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:678 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:672 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/B:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:657 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:657 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:657 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:661 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/B:666 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/B:665 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/B:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:668 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/B:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/B:669 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:699 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:698 5 atoms, 4 bonds, 1 residue, 1 model selected > select add #8/C:697 12 atoms, 10 bonds, 2 residues, 1 model selected > select add #8/C:694 18 atoms, 15 bonds, 3 residues, 1 model selected > select add #8/C:693 26 atoms, 22 bonds, 4 residues, 1 model selected > select add #8/C:692 34 atoms, 29 bonds, 5 residues, 1 model selected > show sel atoms > select #8/C:690 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/C:690 7 atoms, 6 bonds, 1 residue, 1 model selected > select add #8/C:689 18 atoms, 17 bonds, 2 residues, 1 model selected > show sel atoms > select #8/C:689 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/C:689 11 atoms, 11 bonds, 1 residue, 1 model selected > select #8/C:686 9 atoms, 8 bonds, 1 residue, 1 model selected > show sel atoms > show #!4 models > select #8/C:670 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:670 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:670 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:671 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:672 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:671 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:674 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:673 4 atoms, 3 bonds, 1 residue, 1 model selected > select #8/C:672 5 atoms, 4 bonds, 1 residue, 1 model selected > select #8/C:671 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:671 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:670 11 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:669 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:669 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:669 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:669 10 atoms, 10 bonds, 1 residue, 1 model selected > select #8/C:668 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/C:667 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/C:667 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/C:666 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/C:665 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:664 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/C:663 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/C:662 11 atoms, 10 bonds, 1 residue, 1 model selected > open 3fvc Summary of feedback from opening 3fvc fetched from pdb --- note | Fetching compressed mmCIF 3fvc from http://files.rcsb.org/download/3fvc.cif 3fvc title: Crystal structure of a trimeric variant of the Epstein-Barr virus glycoprotein B [more info...] Chain information for 3fvc #9 --- Chain | Description | UniProt A | Glycoprotein GP110 | VGLB_EBV 23-685 Non-standard residues in 3fvc #9 --- NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose (N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE) 3fvc mmCIF Assemblies --- 1| author_and_software_defined_assembly > mmaker #3 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_08_23_12_59_model_0.cif, chain A (#1) with fold_2024_09_02_11_52_model_0.cif, chain A (#3), sequence alignment score = 1481.2 RMSD between 357 pruned atom pairs is 1.205 angstroms; (across all 770 pairs: 19.068) > mmaker #9 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_08_23_12_59_model_0.cif, chain A (#1) with 3fvc, chain A (#9), sequence alignment score = 1612.8 RMSD between 319 pruned atom pairs is 0.942 angstroms; (across all 554 pairs: 3.871) > select #9/A:679 8 atoms, 7 bonds, 1 residue, 1 model selected > hide #!4 models > select #8/A:659 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:666 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/A:667 12 atoms, 12 bonds, 1 residue, 1 model selected > select #9/A:679 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:681 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:678 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:679 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:680 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:679 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:679 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:666 12 atoms, 12 bonds, 1 residue, 1 model selected > select #8/C:201 7 atoms, 7 bonds, 1 residue, 1 model selected > select add #8/C:202 14 atoms, 13 bonds, 2 residues, 1 model selected > show sel atoms > select #8/B:266 8 atoms, 7 bonds, 1 residue, 1 model selected > select add #8/B:267 12 atoms, 10 bonds, 2 residues, 1 model selected > show sel atoms > select #8/A:678 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:692 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:685 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/A:680 8 atoms, 7 bonds, 1 residue, 1 model selected > select #8/C:32 9 atoms, 8 bonds, 1 residue, 1 model selected > select #8/C:415 8 atoms, 7 bonds, 1 residue, 1 model selected > select #9/A:655 11 atoms, 11 bonds, 1 residue, 1 model selected > select #9/A:654 7 atoms, 6 bonds, 1 residue, 1 model selected > select #8/A:655 11 atoms, 11 bonds, 1 residue, 1 model selected > select #9/A:655 11 atoms, 11 bonds, 1 residue, 1 model selected > close > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/KSHVgB/AF3/KSHV_gB_FL/fold_2024_08_23_12_59_model_0.cif Chain information for fold_2024_08_23_12_59_model_0.cif #1 --- Chain | Description A B C | . > save /Users/kjyeol/Desktop/KSHV_gB_FL_AF3_prediction.pdb relModel #1 > select /B:662 11 atoms, 10 bonds, 1 residue, 1 model selected > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/HHV6A/AF3/HHV6A_gB_GS_FL/fold_2024_09_02_11_52_model_0.cif Chain information for fold_2024_09_02_11_52_model_0.cif #2 --- Chain | Description A B C | . > mmaker #2 to #1 Parameters --- Chain pairing | bb Alignment algorithm | Needleman-Wunsch Similarity matrix | BLOSUM-62 SS fraction | 0.3 Gap open (HH/SS/other) | 18/18/6 Gap extend | 1 SS matrix | | | H | S | O ---|---|---|--- H | 6 | -9 | -6 S | | 6 | -6 O | | | 4 Iteration cutoff | 2 Matchmaker fold_2024_08_23_12_59_model_0.cif, chain A (#1) with fold_2024_09_02_11_52_model_0.cif, chain A (#2), sequence alignment score = 1481.2 RMSD between 357 pruned atom pairs is 1.205 angstroms; (across all 770 pairs: 19.068) > hide #1 models > select add #1 19830 atoms, 20253 bonds, 2535 residues, 1 model selected > select #2/C:27 12 atoms, 12 bonds, 1 residue, 1 model selected > select #2/C:20 8 atoms, 7 bonds, 1 residue, 1 model selected > select #2/C:21 12 atoms, 12 bonds, 1 residue, 1 model selected > ui tool show ""Show Sequence Viewer"" > sequence chain #2/A #2/B #2/C Alignment identifier is 1 > select #2/A-C:1 24 atoms, 21 bonds, 3 residues, 1 model selected > select #2/A-C:1-19 444 atoms, 447 bonds, 57 residues, 1 model selected > select #2/A-C:1-19 444 atoms, 447 bonds, 57 residues, 1 model selected > select #2/A-C:22 18 atoms, 15 bonds, 3 residues, 1 model selected > select #2/A-C:1-22 522 atoms, 528 bonds, 66 residues, 1 model selected > close > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/HHV7/AF3/HHV7gB_FL_Trimer/fold_2024_07_24_17_59_model_0.cif Chain information for fold_2024_07_24_17_59_model_0.cif #1 --- Chain | Description A B C | . > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/HHV6A/AF3/HHV6A_gB_GS_FL/fold_2024_09_02_11_52_model_0.cif Chain information for fold_2024_09_02_11_52_model_0.cif #2 --- Chain | Description A B C | . > mmaker #2 to #1 ===== Log before crash end ===== Log: Startup Messages --- warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR bundle with that from NMRSTAR bundle You can double click a model's Name or ID in the model panel to edit those fields UCSF ChimeraX version: 1.7.1 (2024-01-23) © 2016-2023 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/kjyeol/Library/CloudStorage/Box- > Box/JeongRyeolKim/project/SHIELD_ARPA- > H_herpesvirus_gB/HHV6A/AF3/HHV6A_gB_GS_FL/fold_2024_09_02_11_52_model_0.cif Chain information for fold_2024_09_02_11_52_model_0.cif #1 --- Chain | Description A B C | . OpenGL version: 4.1 Metal - 88.1 OpenGL renderer: Apple M1 OpenGL vendor: Apple Python: 3.11.2 Locale: UTF-8 Qt version: PyQt6 6.3.1, Qt 6.3.1 Qt runtime version: 6.3.2 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: MacBookAir10,1 Model Number: MGN63KH/A Chip: Unknown Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 8 GB System Firmware Version: 10151.121.1 OS Loader Version: 10151.121.1 Software: System Software Overview: System Version: macOS 14.5 (23F79) Kernel Version: Darwin 23.5.0 Time since boot: 90 days, 1 hour, 26 minutes Graphics/Displays: Apple M1: Chipset Model: Apple M1 Type: GPU Bus: Built-In Total Number of Cores: 7 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-In Retina LCD Resolution: 2560 x 1600 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal Installed Packages: alabaster: 0.7.16 appdirs: 1.4.4 appnope: 0.1.3 asttokens: 2.4.1 Babel: 2.14.0 backcall: 0.2.0 beautifulsoup4: 4.11.2 blockdiag: 3.0.0 blosc2: 2.0.0 build: 0.10.0 certifi: 2022.12.7 cftime: 1.6.3 charset-normalizer: 3.3.2 ChimeraX-AddCharge: 1.5.13 ChimeraX-AddH: 2.2.5 ChimeraX-AlignmentAlgorithms: 2.0.1 ChimeraX-AlignmentHdrs: 3.4.1 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.12.2 ChimeraX-AlphaFold: 1.0 ChimeraX-AltlocExplorer: 1.1.1 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.49.1 ChimeraX-AtomicLibrary: 12.1.5 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.3.2 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 2.1.2 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.10.5 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.2.2 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.3.2 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.3.2 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.2.4 ChimeraX-ColorActions: 1.0.3 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.5 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.7.1 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.2 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2 ChimeraX-DistMonitor: 1.4 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.1.1 ChimeraX-Hbonds: 2.4 ChimeraX-Help: 1.2.2 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.1 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-Label: 1.1.8 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.1.6 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.1.4 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.2 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.6.1 ChimeraX-MedicalToolbar: 1.0.2 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.12.1 ChimeraX-MMTF: 2.2 ChimeraX-Modeller: 1.5.14 ChimeraX-ModelPanel: 1.4 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.1 ChimeraX-NRRD: 1.1 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.13.1 ChimeraX-PDB: 2.7.3 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1 ChimeraX-PubChem: 2.1 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.1 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.2 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.11 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.1.1 ChimeraX-ShowSequences: 1.0.2 ChimeraX-SideView: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.12.4 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.1.2 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.2.2 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.1.2 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.33.3 ChimeraX-uniprot: 2.3 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.3.2 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.3 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.1 contourpy: 1.2.0 cxservices: 1.2.2 cycler: 0.12.1 Cython: 0.29.33 debugpy: 1.8.0 decorator: 5.1.1 docutils: 0.19 executing: 2.0.1 filelock: 3.9.0 fonttools: 4.47.2 funcparserlib: 2.0.0a0 glfw: 2.6.4 grako: 3.16.5 h5py: 3.10.0 html2text: 2020.1.16 idna: 3.6 ihm: 0.38 imagecodecs: 2023.9.18 imagesize: 1.4.1 ipykernel: 6.23.2 ipython: 8.14.0 ipython-genutils: 0.2.0 ipywidgets: 8.1.1 jedi: 0.18.2 Jinja2: 3.1.2 jupyter-client: 8.2.0 jupyter-core: 5.7.1 jupyterlab-widgets: 3.0.9 kiwisolver: 1.4.5 line-profiler: 4.0.2 lxml: 4.9.2 lz4: 4.3.2 MarkupSafe: 2.1.4 matplotlib: 3.7.2 matplotlib-inline: 0.1.6 msgpack: 1.0.4 nest-asyncio: 1.6.0 netCDF4: 1.6.2 networkx: 3.1 nibabel: 5.0.1 nptyping: 2.5.0 numexpr: 2.8.8 numpy: 1.25.1 openvr: 1.23.701 packaging: 21.3 ParmEd: 3.4.3 parso: 0.8.3 pep517: 0.13.0 pexpect: 4.9.0 pickleshare: 0.7.5 pillow: 10.2.0 pip: 23.0 pkginfo: 1.9.6 platformdirs: 4.1.0 prompt-toolkit: 3.0.43 psutil: 5.9.5 ptyprocess: 0.7.0 pure-eval: 0.2.2 py-cpuinfo: 9.0.0 pycollada: 0.7.2 pydicom: 2.3.0 Pygments: 2.16.1 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.2801 pyparsing: 3.0.9 pyproject-hooks: 1.0.0 PyQt6-commercial: 6.3.1 PyQt6-Qt6: 6.3.2 PyQt6-sip: 13.4.0 PyQt6-WebEngine-commercial: 6.3.1 PyQt6-WebEngine-Qt6: 6.3.2 python-dateutil: 2.8.2 pytz: 2023.3.post1 pyzmq: 25.1.2 qtconsole: 5.4.3 QtPy: 2.4.1 RandomWords: 0.4.0 requests: 2.31.0 scipy: 1.11.1 setuptools: 67.4.0 setuptools-scm: 7.0.5 sfftk-rw: 0.7.3 six: 1.16.0 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.5 sphinx: 6.1.3 sphinx-autodoc-typehints: 1.22 sphinxcontrib-applehelp: 1.0.8 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 1.0.6 sphinxcontrib-htmlhelp: 2.0.5 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 1.0.7 sphinxcontrib-serializinghtml: 1.1.10 stack-data: 0.6.3 superqt: 0.5.0 tables: 3.8.0 tcia-utils: 1.5.1 tifffile: 2023.7.18 tinyarray: 1.2.4 tomli: 2.0.1 tornado: 6.4 traitlets: 5.9.0 typing-extensions: 4.9.0 tzdata: 2023.4 urllib3: 2.1.0 wcwidth: 0.2.13 webcolors: 1.12 wheel: 0.38.4 wheel-filename: 1.4.1 widgetsnbextension: 4.0.9 }}} " defect closed normal Core duplicate Tom Goddard all ChimeraX