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Opened 4 months ago
Closed 4 months ago
#18251 closed defect (can't reproduce)
Crash opening .cif
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-15.5-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Thread 0x00000003587bb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 320 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 765 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 768 in get
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1678 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/tasks.py", line 300 in _run_function
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 0x00000003577af000 (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 0x00000003567a3000 (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 0x0000000355797000 (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 0x000000035478b000 (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 0x000000035377f000 (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 0x0000000352773000 (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 0x0000000351767000 (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 0x000000035075b000 (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 0x000000034f74f000 (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 0x000000034e743000 (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 0x000000034d737000 (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 0x000000034c72b000 (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 0x000000034b71f000 (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 0x000000034a713000 (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 0x0000000349707000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py", line 962 in getaddrinfo
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/util/connection.py", line 60 in create_connection
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py", line 199 in _new_conn
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py", line 279 in connect
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 979 in send
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1041 in _send_output
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1281 in endheaders
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connection.py", line 441 in request
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 495 in _make_request
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/connectionpool.py", line 789 in urlopen
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/poolmanager.py", line 443 in urlopen
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/_request_methods.py", line 182 in request_encode_url
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/urllib3/_request_methods.py", line 135 in request
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/cxservices/rest.py", line 206 in request
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/cxservices/rest.py", line 228 in GET
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/cxservices/api_client.py", line 341 in request
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/cxservices/api_client.py", line 151 in __call_api
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 125 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 0x00000003484ff000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1134 in read
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ssl.py", line 1278 in recv_into
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/socket.py", line 706 in readinto
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 279 in _read_status
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 318 in begin
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/http/client.py", line 1378 in getresponse
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1352 in do_open
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 1391 in https_open
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 496 in _call_chain
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 536 in _open
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 519 in open
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/urllib/request.py", line 216 in urlopen
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/available.py", line 62 in load
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 516 in reload_available
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x000000020d1f1f00 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 54 in open
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 497 in remember_data_format
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 526 in collated_open
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 215 in provider_open
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 132 in cmd_open
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 3213 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 2117 in _open_dropped_file
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 293 in event
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, cython.cimports.libc.math, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.linalg._fblas, scipy.linalg._flapack, scipy.linalg.cython_lapack, scipy.linalg._cythonized_array_utils, scipy.linalg._solve_toeplitz, scipy.linalg._decomp_lu_cython, scipy.linalg._matfuncs_sqrtm_triu, scipy.linalg.cython_blas, scipy.linalg._matfuncs_expm, scipy.linalg._decomp_update, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, scipy.sparse.linalg._propack._spropack, scipy.sparse.linalg._propack._dpropack, scipy.sparse.linalg._propack._cpropack, scipy.sparse.linalg._propack._zpropack, scipy.sparse.csgraph._tools, scipy.sparse.csgraph._shortest_path, scipy.sparse.csgraph._traversal, scipy.sparse.csgraph._min_spanning_tree, scipy.sparse.csgraph._flow, scipy.sparse.csgraph._matching, scipy.sparse.csgraph._reordering, scipy.spatial._ckdtree, scipy._lib.messagestream, scipy.spatial._qhull, scipy.spatial._voronoi, scipy.spatial._distance_wrap, scipy.spatial._hausdorff, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, scipy.special._ellip_harm_2, scipy.spatial.transform._rotation, markupsafe._speedups, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, lxml._elementpath, lxml.etree, chimerax.surface._surface, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 91)
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===== Log before crash start =====
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
> open /Users/keshavkishor/Desktop/MGAT6/mgat4c.pdb
Chain information for mgat4c.pdb #1
---
Chain | Description
A | No description available
> select ::name="L01"::name="L02"::name="MN"
144 atoms, 152 bonds, 3 residues, 1 model selected
> show sel target ab
> style sel ball
Changed 144 atom styles
> color sel byhetero
> color sel lime
> color sel cyan
> color sel byhetero
> select clear
> hide atoms
> show atoms
> hide cartoons
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
3734 atoms, 3832 bonds, 464 residues, 1 model selected
> hide sel atoms
> style sel stick
Changed 3734 atom styles
Drag select of 144 atoms, 152 bonds
> style sel stick
Changed 144 atom styles
> style sel sphere
Changed 144 atom styles
> style sel ball
Changed 144 atom styles
> style sel stick
Changed 144 atom styles
> set bgColor white
> set bgColor black
> set bgColor white
> lighting soft
> lighting full
> lighting simple
> ui tool show "Selection Inspector"
> view sel
> select clear
> close
> open /Users/keshavkishor/Desktop/MGAT6/mgat4c.pdb format pdb
Chain information for mgat4c.pdb #1
---
Chain | Description
A | No description available
> select /A
3734 atoms, 3832 bonds, 464 residues, 1 model selected
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
3734 atoms, 3832 bonds, 464 residues, 1 model selected
> hide sel atoms
> select ::name="MN"
1 atom, 1 residue, 1 model selected
> style sel sphere
Changed 1 atom style
> select ::name="L01"
104 atoms, 111 bonds, 1 residue, 1 model selected
> color sel cyan
> color sel byhetero
> style sel ball
Changed 104 atom styles
> style sel stick
Changed 104 atom styles
> nucleotides sel atoms
> style nucleic & sel stick
Changed 0 atom styles
> select ::name="L01"
104 atoms, 111 bonds, 1 residue, 1 model selected
> select ::name="L02"
39 atoms, 41 bonds, 1 residue, 1 model selected
> color sel hot pink
> color sel byhetero
> select clear
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
3734 atoms, 3832 bonds, 464 residues, 1 model selected
> show sel surfaces
> hide sel surfaces
> ui tool show "Show Sequence Viewer"
> sequence chain /A
Alignment identifier is 1/A
> select clear
> select /A:210
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /A:210-212
25 atoms, 24 bonds, 3 residues, 1 model selected
> show sel atoms
> label (#!1 & sel) attribute name
> style sel ball
Changed 25 atom styles
> style sel stick
Changed 25 atom styles
> select clear
> save /Users/keshavkishor/Desktop/MGAT6/mgatc4c.pdb serialNumbering amber
> open /Users/keshavkishor/Desktop/MGAT6/Try/N-glycan.pdb
> /Users/keshavkishor/Desktop/MGAT6/Try/mgat4c_v2.pdb
Chain information for mgat4c_v2.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> close #1
> hide #3 models
> select all
4079 atoms, 4190 bonds, 476 residues, 2 models selected
> select H
97 atoms, 9 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #2/?:4@O6
1 atom, 1 residue, 1 model selected
> select add #2/?:7@C1
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> select clear
> select add #3
3878 atoms, 3984 bonds, 467 residues, 1 model selected
> select add #2
3982 atoms, 4094 bonds, 476 residues, 2 models selected
> matchmaker #2 to #3
No matrix compatible with both reference structure and all match structures
> show #3 models
> open 5vcm fromDatabase uniprot_variants format variants
Fetching url https://www.ebi.ac.uk/proteins/api/variation/5vcm failed:
HTTP Error 400: Bad Request
> close #2
> hide sel cartoons
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
3734 atoms, 3832 bonds, 464 residues, 1 model selected
> hide sel atoms
> view sel
No displayed objects specified.
> show sel cartoons
> select clear
> ui tool show ViewDockX
No suitable models found for ViewDockX
> hide cartoons
Drag select of 104 atoms, 111 bonds
> delete sel
> show cartoons
> save /Users/keshavkishor/Desktop/MGAT6/Try/receptor.pdb relModel #3
> open /Users/keshavkishor/Desktop/MGAT6/Try/mgat4c_v2.pdb
Chain information for mgat4c_v2.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> hide #1 models
> show #1 models
> hide #3 models
> hide #1 cartoons
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
7468 atoms, 7664 bonds, 928 residues, 2 models selected
> hide sel & #1 atoms
> show #3 models
> show sel surfaces
> hide sel surfaces
> show sel surfaces
> hide sel surfaces
> open /Users/keshavkishor/Desktop/MGAT6/Try/output_models.pdbqt
Summary of feedback from opening
/Users/keshavkishor/Desktop/MGAT6/Try/output_models.pdbqt
---
warnings | Ignored bad PDB record found on line 2
REMARK VINA RESULT: -5.7 0.000 0.000
Ignored bad PDB record found on line 3
REMARK WARNING: 32 MAX_TORS EXCEEDED!!!
Ignored bad PDB record found on line 5
REMARK status: ('A' for Active; 'I' for Inactive)
Ignored bad PDB record found on line 6
REMARK 1 A between atoms: O1_2 and C1_3
Ignored bad PDB record found on line 7
REMARK 2 A between atoms: C5_5 and C6_6
2995 messages similar to the above omitted
Opened output_models.pdbqt containing 20 structures (2600 atoms, 2560 bonds)
> viewdockx #2.1-20
> hide sel cartoons
> hide #!2 models
> show #!2 models
> hide #!2 models
> hide #2.1 models
> show #2.1 models
> hide #2.1-20#!3 target m
> select add #2
10068 atoms, 10224 bonds, 1208 residues, 25 models selected
> show #2.1 models
> show #2.2 models
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> hide #2.2 models
Cell requested for row 0 is out of bounds for table with 0 rows! Resizing
table model.
> show #2.2 target m
> hide #2.1 target m
> show #2.3 target m
> hide #2.2 target m
> show #2.4 target m
> hide #2.3 target m
> show #2.5 target m
> hide #2.4 target m
> show #2.6 target m
> hide #2.5 target m
> show #2.7 target m
> hide #2.6 target m
> show #2.8 target m
> hide #2.7 target m
> show #2.9 target m
> hide #2.8 target m
> show #2.10 target m
> hide #2.9 target m
> show #2.11 target m
> hide #2.10 target m
> show #2.12 target m
> hide #2.11 target m
> show #2.13 target m
> hide #2.12 target m
> show #2.14 target m
> hide #2.13 target m
> show #2.15 target m
> hide #2.14 target m
> show #2.16 target m
> hide #2.15 target m
> show #2.17 target m
> hide #2.16 target m
> show #2.18 target m
> hide #2.17 target m
> show #2.19 target m
> hide #2.18 target m
> show #2.20 target m
> hide #2.19 target m
> show #2.19 target m
> hide #2.20 target m
> show #2.20 target m
> hide #2.19 target m
> show #!3 target m
> hide #2.20 target m
> show #2.1 target m
> hide #!3 target m
Cell requested for row 1 is out of bounds for table with 23 rows! Resizing
table model.
> hide #!2 models
> select subtract #2
7468 atoms, 7664 bonds, 928 residues, 4 models selected
> open /Users/keshavkishor/Desktop/MGAT6/Try/ligand.pdb
Cell requested for row 1 is out of bounds for table with 4 rows! Resizing
table model.
> select add #4
7669 atoms, 7870 bonds, 937 residues, 5 models selected
Drag select of 74 atoms, 80 bonds
> select clear
Drag select of 104 atoms, 111 bonds
> display H sel
> show H sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show H sel
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> show H
> show sel target ab
> select clear
Drag select of 201 atoms, 206 bonds
> select H
617 atoms, 249 residues, 21 models selected
> delete atoms (#4 & sel)
> delete bonds (#4 & sel)
> select #4/?:9@C1
1 atom, 1 residue, 1 model selected
> select add #4/?:7@O6
2 atoms, 2 residues, 1 model selected
> bond sek
Missing or invalid "atoms" argument: invalid atoms specifier
> bond sel
Created 1 bond
> select clear
> select #4/?:7@C1
1 atom, 1 residue, 1 model selected
> select add #4/?:4@O6
2 atoms, 2 residues, 1 model selected
> bond sel
Created 1 bond
> select clear
> open
> /Users/keshavkishor/Desktop/MGAT6/Try/72e2a1c9-3a4d-485e-ab96-1009f48b987b/all.pdb
Summary of feedback from opening
/Users/keshavkishor/Desktop/MGAT6/Try/72e2a1c9-3a4d-485e-ab96-1009f48b987b/all.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK GENERATED BY Re-Glyco from GlycoShape
Ignored bad PDB record found on line 2
REMARK Time 2025-07-22-14:06:15
Ignored bad PDB record found on line 3
REMARK ______ _______ _______ ___ __ __ _______ _______
Ignored bad PDB record found on line 5
REMARK| | || | ___| ____ | ___|| | | |_| || || _ |
Ignored bad PDB record found on line 6
REMARK| |_||_ | |___ |____| | | __ | | | || || | | |
611 messages similar to the above omitted
Chain information for all.pdb
---
Chain | Description
5.1/A 5.2/A 5.3/A 5.4/A 5.5/A 5.6/A 5.7/A 5.8/A 5.9/A 5.10/A 5.11/A 5.12/A 5.13/A 5.14/A 5.15/A 5.16/A 5.17/A 5.18/A 5.19/A 5.20/A 5.21/A 5.22/A 5.23/A 5.24/A 5.25/A 5.26/A 5.27/A 5.28/A 5.29/A 5.30/A 5.31/A 5.32/A 5.33/A 5.34/A 5.35/A 5.36/A 5.37/A 5.38/A 5.39/A 5.40/A 5.41/A 5.42/A 5.43/A 5.44/A 5.45/A 5.46/A 5.47/A 5.48/A 5.49/A 5.50/A | No description available
Computing secondary structure
> hide #4 models
> hide #!1 models
> select all
199856 atoms, 204928 bonds, 24522 residues, 75 models selected
> show sel & #5.1-50 cartoons
> select
> ::name="0YB"::name="2MA"::name="4YB"::name="L01"::name="L02"::name="MN"::name="ROH"::name="VMB"::name="XMA"
5688 atoms, 5664 bonds, 394 residues, 73 models selected
> show sel & #5.1-50 atoms
> close #5
> show #4 models
> show #!3 models
> show #!2 models
> show #!1 models
Cell requested for row 1 is out of bounds for table with 5 rows! Resizing
table model.
> close #2
> close #1
> select all
3878 atoms, 3984 bonds, 475 residues, 2 models selected
> show sel cartoons
> open /Users/keshavkishor/Desktop/MGAT6/Try/mgat4c_v2.pdb
Chain information for mgat4c_v2.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
7468 atoms, 7664 bonds, 928 residues, 2 models selected
> hide sel atoms
> show sel cartoons
> hide sel cartoons
Drag select of 80 atoms, 82 bonds
> hide sel atoms
Drag select of 104 atoms, 111 bonds
Drag select of 2 bonds
Drag select of 104 atoms, 111 bonds
> ui mousemode right "move picked models"
> ui mousemode right "translate selected models"
Drag select of 5 atoms, 8 bonds
Drag select of 104 atoms, 111 bonds
> ui mousemode right "translate selected models"
Drag select of 3 atoms, 4 bonds
Drag select of 104 atoms, 111 bonds
> select clear
> hide #!3 models
> close #3
Drag select of 104 atoms, 111 bonds
> save /Users/keshavkishor/Desktop/MGAT6/Try/n-glycan_alphafold.pdb
> selectedOnly true
Computing secondary structure
> open /Users/keshavkishor/Desktop/MGAT6/Try/n-glycan_alphafold.pdb
Summary of feedback from opening
/Users/keshavkishor/Desktop/MGAT6/Try/n-glycan_alphafold.pdb
---
warnings | Cannot find LINK/SSBOND residue ROH (1 )
Cannot find LINK/SSBOND residue 4YB (2 )
Cannot find LINK/SSBOND residue 4YB (3 )
Cannot find LINK/SSBOND residue VMB (4 )
Cannot find LINK/SSBOND residue 2MA (5 )
3 messages similar to the above omitted
> select add #1
3878 atoms, 3984 bonds, 467 residues, 1 model selected
> select subtract #1
Nothing selected
> hide #1 models
> close #1
> tile
2 models tiled
> select ~sel & ##selected
Nothing selected
> ~tile
> select #4/?:2@C1
1 atom, 1 residue, 1 model selected
> select add #4/?:2@C2
2 atoms, 1 residue, 1 model selected
> select add #4/?:2@C3
3 atoms, 1 residue, 1 model selected
> select add #4/?:2@C4
4 atoms, 1 residue, 1 model selected
> select add #4/?:2@C5
5 atoms, 1 residue, 1 model selected
> select add #4/?:2@C6
6 atoms, 1 residue, 1 model selected
> select add #4/?:2@O6
7 atoms, 1 residue, 1 model selected
> select add #2/C:1@C5
8 atoms, 2 residues, 2 models selected
> select subtract #2/C:1@C5
7 atoms, 1 residue, 1 model selected
> select add #2/C:1@C7
8 atoms, 2 residues, 2 models selected
> select add #2/C:1@C3
9 atoms, 2 residues, 2 models selected
> select add #2/C:1@C4
10 atoms, 2 residues, 2 models selected
> select add #2/C:1@C5
11 atoms, 2 residues, 2 models selected
> select add #2/C:1@C6
12 atoms, 2 residues, 2 models selected
> select add #2/C:1@C8
13 atoms, 2 residues, 2 models selected
> select add #2/C:1@O4
14 atoms, 2 residues, 2 models selected
> matchmaker #2to #4 sel
Missing or invalid "matchAtoms" argument: only initial part "#2" of atom
specifier valid
> matchmaker #2 to #4 sel
Expected a keyword
> matchmaker #2:sel to #4:sel
No 'to' model specified
> align #2:sel toAtoms #4:sel
No atoms paired for alignment
> align #2:C,N,O toAtoms #4:C,N,O
No atoms paired for alignment
> cofr #2
> select clear
Drag select of 104 atoms, 111 bonds
> view matrix models
> #4,0.96143,-0.27435,0.019454,-0.071193,0.14538,0.44686,-0.88271,-30.98,0.23348,0.8515,0.46951,-43.27
> view matrix models
> #4,0.96143,-0.27435,0.019454,-2.4603,0.14538,0.44686,-0.88271,-29.436,0.23348,0.8515,0.46951,-44.862
> ui mousemode right rotate
Drag select of 1 atoms
> view sel
> hide #2 models
> show #2 models
> hide #4 models
> select add #4
104 atoms, 111 bonds, 9 residues, 1 model selected
> show #4 models
> ui mousemode right "rotate selected models"
> select clear
> select #2
104 atoms, 111 bonds, 1 residue, 1 model selected
> select subtract #2
Nothing selected
> hide #2 models
> select add #4
104 atoms, 111 bonds, 9 residues, 1 model selected
> view matrix models
> #4,0.96635,-0.25563,0.028492,-2.7695,0.15932,0.50791,-0.84655,-30.367,0.20193,0.82261,0.53155,-43.51
> view matrix models
> #4,0.96904,-0.23845,0.064085,-2.8705,0.18131,0.51101,-0.84023,-30.804,0.1676,0.82584,0.53843,-42.851
> ui mousemode right "move picked models"
> show #2 models
> select add #2
208 atoms, 222 bonds, 10 residues, 2 models selected
> select subtract #2
104 atoms, 111 bonds, 9 residues, 1 model selected
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.96904,-0.23845,0.064085,-3.3232,0.18131,0.51101,-0.84023,-30.945,0.1676,0.82584,0.53843,-43.173
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.79164,-0.39213,-0.46856,-0.5965,0.27999,0.91444,-0.29223,-35.561,0.54306,0.10015,0.8337,-38.701
> view matrix models
> #4,0.88137,-0.43839,-0.17608,-0.11339,0.30552,0.8132,-0.49534,-35.733,0.36034,0.38278,0.85067,-39.023
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.88137,-0.43839,-0.17608,-1.2122,0.30552,0.8132,-0.49534,-35.012,0.36034,0.38278,0.85067,-39.816
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.76939,-0.49904,-0.39875,0.6116,0.38331,0.86004,-0.33675,-36.324,0.51099,0.10625,0.85299,-38.853
> view matrix models
> #4,0.869,-0.49447,-0.018558,0.66358,0.41378,0.74673,-0.52075,-36.32,0.27135,0.44485,0.85351,-38.942
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.869,-0.49447,-0.018558,0.20345,0.41378,0.74673,-0.52075,-36.204,0.27135,0.44485,0.85351,-39.273
> select clear
> close #2
> open /Users/keshavkishor/Desktop/MGAT6/Try/mgat4c_v2.pdb
Chain information for mgat4c_v2.pdb #1
---
Chain | Description
A | No description available
Computing secondary structure
> close #1
> open /Users/keshavkishor/Desktop/MGAT6/mgat4c.pdb
Chain information for mgat4c.pdb #1
---
Chain | Description
A | No description available
> select
> ::name="0YB"::name="2MA"::name="4YB"::name="L01"::name="L02"::name="MN"::name="ROH"::name="VMB"::name="XMA"
248 atoms, 263 bonds, 12 residues, 2 models selected
> show sel target ab
> view matrix models
> #4,0.869,-0.49447,-0.018558,8.3209,0.41378,0.74673,-0.52075,-34.067,0.27135,0.44485,0.85351,-59.663,#1,1,0,0,8.1174,0,1,0,2.137,0,0,1,-20.39
> view matrix models
> #4,0.869,-0.49447,-0.018558,11.644,0.41378,0.74673,-0.52075,-35.206,0.27135,0.44485,0.85351,-64.232,#1,1,0,0,11.44,0,1,0,0.99771,0,0,1,-24.96
> hide sel cartoons
Drag select of 403 atoms, 400 bonds, 454 residues
> hide sel cartoons
Drag select of 484 atoms, 492 bonds, 10 residues
> hide sel cartoons
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
3734 atoms, 3832 bonds, 464 residues, 1 model selected
> hide sel atoms
> view matrix models #1,1,0,0,3.4443,0,1,0,-7.6297,0,0,1,-33.244
> undo
> select clear
Drag select of 40 atoms, 41 bonds
> hide sel atoms
> view matrix models #1,1,0,0,8.1148,0,1,0,5.1281,0,0,1,-11.119
> undo
> select clear
Drag select of 104 atoms, 111 bonds
> view matrix models
> #4,0.869,-0.49447,-0.018558,-8.2426,0.41378,0.74673,-0.52075,-31.047,0.27135,0.44485,0.85351,-13.652
> view sel
> view matrix models
> #4,0.869,-0.49447,-0.018558,-5.1187,0.41378,0.74673,-0.52075,-29.845,0.27135,0.44485,0.85351,-16.006
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.29976,-0.36158,-0.88284,-0.5874,0.87669,0.46936,0.10543,-31.57,0.37625,-0.80558,0.45769,-2.6517
> view matrix models
> #4,0.22894,-0.14589,-0.96245,-2.6647,0.95735,0.21279,0.19548,-29.055,0.17628,-0.96615,0.18838,2.0299
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.22894,-0.14589,-0.96245,-2.6535,0.95735,0.21279,0.19548,-29.109,0.17628,-0.96615,0.18838,1.9173
> view matrix models
> #4,0.22894,-0.14589,-0.96245,-0.11983,0.95735,0.21279,0.19548,-32.355,0.17628,-0.96615,0.18838,-7.6471
> view matrix models
> #4,0.22894,-0.14589,-0.96245,1.8764,0.95735,0.21279,0.19548,-31.875,0.17628,-0.96615,0.18838,-5.943
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.23212,-0.16177,-0.95914,2.055,0.9579,0.20929,0.19653,-31.831,0.16895,-0.96438,0.20354,-5.7437
> view matrix models
> #4,0.24008,-0.20435,-0.949,2.552,0.95926,0.19995,0.19962,-31.71,0.14896,-0.95826,0.24403,-5.2228
> view matrix models
> #4,0.24192,-0.2149,-0.9462,2.6792,0.95956,0.19764,0.20045,-31.679,0.14393,-0.95643,0.25402,-5.0969
> ui mousemode right "move picked models"
> undo
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.24008,-0.20435,-0.949,3.7429,0.95926,0.19995,0.19962,-31.437,0.14896,-0.95826,0.24403,-4.843
> view sel
> view matrix models
> #4,0.24008,-0.20435,-0.949,3.6817,0.95926,0.19995,0.19962,-31.471,0.14896,-0.95826,0.24403,-5.8141
> view matrix models
> #4,0.24008,-0.20435,-0.949,3.6549,0.95926,0.19995,0.19962,-31.479,0.14896,-0.95826,0.24403,-5.9146
> view matrix models
> #4,0.24008,-0.20435,-0.949,3.2402,0.95926,0.19995,0.19962,-31.567,0.14896,-0.95826,0.24403,-5.7042
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.24008,-0.20435,-0.949,1.0042,0.95926,0.19995,0.19962,-34.5,0.14896,-0.95826,0.24403,-5.5825
> select clear
> select #2
Nothing selected
> select #4
104 atoms, 111 bonds, 9 residues, 1 model selected
> view matrix models
> #4,0.24008,-0.20435,-0.949,0.48683,0.95926,0.19995,0.19962,-35.534,0.14896,-0.95826,0.24403,-4.9841
> view matrix models
> #4,0.24008,-0.20435,-0.949,3.7318,0.95926,0.19995,0.19962,-36.915,0.14896,-0.95826,0.24403,-4.6404
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.89817,-0.31134,0.31041,-0.75709,0.28021,0.94945,0.14149,-34.546,-0.33877,-0.0401,0.94001,-4.284
> ui mousemode right "translate selected models"
> view matrix models
> #4,0.89817,-0.31134,0.31041,-0.5477,0.28021,0.94945,0.14149,-34.657,-0.33877,-0.0401,0.94001,-4.2497
> ui mousemode right rotate
> ui mousemode right "translate selected models"
> ui mousemode right "rotate selected models"
> view matrix models
> #4,0.90633,-0.29414,0.30339,-0.98509,0.26344,0.95467,0.13856,-34.421,-0.33039,-0.045652,0.94274,-4.3198
> view matrix models
> #4,0.88807,-0.33142,0.31858,-0.026101,0.29982,0.9429,0.14511,-34.927,-0.34848,-0.033353,0.93672,-4.1735
> select clear
> hide #1 models
Drag select of 72 atoms, 79 bonds
Drag select of 2 atoms, 1 bonds
Drag select of 1 atoms, 1 bonds
> show #1 models
> view matrix models
> #4,0.90883,-0.30588,0.28366,-0.97535,0.29466,0.95203,0.082552,-35.292,-0.2953,0.0085574,0.95536,-5.693
> select clear
> open /Users/keshavkishor/Desktop/MGAT6/with_only_Mn/protein.pdb
Chain information for protein.pdb #2
---
Chain | Description
A | No description available
Computing secondary structure
> hide #1 models
> hide #2 models
> hide #4 models
> select add #2
3735 atoms, 3834 bonds, 465 residues, 1 model selected
> view sel
> show #2 models
> view sel
> view matrix models
> #2,0.84168,-0.099193,0.53079,-0.27156,0.095195,0.99484,0.034964,0.33266,-0.53152,0.0211,0.84678,-1.8373
> select
> ::name="ALA"::name="ARG"::name="ASN"::name="ASP"::name="CYS"::name="CYX"::name="GLN"::name="GLU"::name="GLY"::name="HIS"::name="ILE"::name="LEU"::name="LYS"::name="MET"::name="PHE"::name="PRO"::name="SER"::name="THR"::name="TRP"::name="TYR"::name="VAL"
7468 atoms, 7666 bonds, 928 residues, 2 models selected
> hide sel & #2 atoms
> select add #1
7612 atoms, 7818 bonds, 931 residues, 2 models selected
> select subtract #1
3734 atoms, 3834 bonds, 464 residues, 1 model selected
> select clear
> open /Users/keshavkishor/Desktop/MGAT6/mgat4c.cif
===== 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 - 89.4
OpenGL renderer: Apple M3 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: en_US.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: Mac15,6
Model Number: MRX43LL/A
Chip: Apple M3 Pro
Total Number of Cores: 12 (6 performance and 6 efficiency)
Memory: 18 GB
System Firmware Version: 11881.121.1
OS Loader Version: 11881.121.1
Software:
System Software Overview:
System Version: macOS 15.5 (24F74)
Kernel Version: Darwin 24.5.0
Time since boot: 3 days, 56 minutes
Graphics/Displays:
Apple M3 Pro:
Chipset Model: Apple M3 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 18
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
VX3418-2KPC:
Resolution: 3440 x 1440 (UWQHD - Ultra-Wide Quad HD)
UI Looks like: 3440 x 1440 @ 180.00Hz
Main Display: Yes
Mirror: Off
Online: Yes
Rotation: Supported
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
autocommand: 2.2.2
babel: 2.16.0
backports.tarfile: 1.2.0
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-AllMetal3D: 0.8
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-Clipper: 0.24.0
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-ISOLDE: 1.9
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
fsspec: 2025.5.1
funcparserlib: 2.0.0a0
glfw: 2.8.0
gradio_client: 0.11.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
hf-xet: 1.1.3
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
huggingface-hub: 0.32.5
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
importlib_resources: 6.4.0
inflect: 7.3.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
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: 3.10.1
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
more-itertools: 10.3.0
msgpack: 1.0.8
narwhals: 1.30.0
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: 2.2.3
numpy: 1.26.4
openvr: 1.26.701
ordered-set: 4.1.0
packaging: 23.2
packaging: 24.1
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
platformdirs: 4.2.2
plotly: 6.0.0
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
pyKVFinder: 0.7.3
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
PyYAML: 6.0.2
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
Send2Trash: 1.8.3
SEQCROW: 1.8.21
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
toml: 0.10.2
tomli: 2.0.1
tornado: 6.4.2
tqdm: 4.67.1
traitlets: 5.14.3
typeguard: 4.3.0
typing_extensions: 4.12.2
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
websockets: 11.0.3
wheel: 0.43.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
zipp: 3.19.2
Change History (2)
comment:1 by , 4 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash opening .cif |
comment:2 by , 4 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | assigned → closed |
Need errant file to reproduce.
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Possibly small-molecule CIF