id	summary	reporter	owner	description	type	status	priority	milestone	component	version	resolution	keywords	cc	blockedby	blocking	notify_on_close	platform	project
16607	Crash moving window between screens(?)	chimerax-bug-report@…	Tom Goddard	"{{{
The following bug report has been submitted:
Platform:        macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault

Thread 0x000000033379b000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 324 in wait
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 622 in wait
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1392 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000302013000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 579 in _handle_results
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000301007000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 531 in _handle_tasks
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000017fedf000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py"", line 415 in select
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py"", line 930 in wait
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/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 ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 522 in _handle_workers
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000017eed3000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000017dec7000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000017cebb000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000017beaf000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x000000017aea3000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000179e97000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000178e8b000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Thread 0x0000000177e7f000 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py"", line 114 in worker
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 975 in run
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 1038 in _bootstrap_inner
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py"", line 995 in _bootstrap

Current thread 0x00000001f575cf40 (most recent call first):
  File ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/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 ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/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 ""/private/var/folders/qn/1543jkwn4v1b9mv5kwh30t700000gn/T/AppTranslocation/4958E66E-AF5F-4C5C-9AFE-9BCD374CD613/d/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, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.pdb_lib._load_libs, 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.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, PIL._imagingmath, cython.cimports.libc.math, scipy._lib._ccallback_c, 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._sparsetools, _csparsetools, scipy.sparse._csparsetools, 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.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, scipy.optimize._lbfgsb, _moduleTNC, scipy.optimize._moduleTNC, scipy.optimize._cobyla, scipy.optimize._slsqp, scipy.optimize._minpack, scipy.optimize._lsq.givens_elimination, scipy.optimize._zeros, scipy.optimize._highs.cython.src._highs_wrapper, scipy.optimize._highs._highs_wrapper, scipy.optimize._highs.cython.src._highs_constants, scipy.optimize._highs._highs_constants, scipy.linalg._interpolative, scipy.optimize._bglu_dense, scipy.optimize._lsap, scipy.spatial._ckdtree, 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, scipy.optimize._direct, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.mlp._mlp (total: 114)


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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/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
> (1)/ligands_dir/ligand_Parkin_5c1z_l.pdb""

Chain information for ligand_Parkin_5c1z_l.pdb #1  
---  
Chain | Description  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> style cartoon

Expected a keyword  

> cartoon smoothloops true

Expected an atoms specifier or a keyword  

> cartoon hide backbone

> color tan # Set entire structure to tan (or other base color)

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red :50 # Highlight residue 50 in red (example)

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color blue :.A # Set chain A to blue (if multiple chains are present)

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> select /B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> select /B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> sequence chain #1/B

Alignment identifier is 1/B  

> open ""/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
> (1)/ligands_dir/ligand_Parkin_5c1z_l.pdb""

Chain information for ligand_Parkin_5c1z_l.pdb #2  
---  
Chain | Description  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> style cartoon

Expected a keyword  

> style cartoon

Expected a keyword  

> color tan # Set entire structure to tan (or other base color)

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color red :50 # Highlight residue 50 in red (example)

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color blue :.A # Set chain A to blue (if multiple chains are present)

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> style sel stick

Changed 6036 atom styles  

> style sel sphere

Changed 6036 atom styles  

> style sel sphere

Changed 6036 atom styles  

> open ""/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
> (1)/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb""

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
(1)/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2126.52  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 42.04  
  
Chain information for model_1.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> hide #!1 models

> hide #!2 models

> select add #3

29511 atoms, 30054 bonds, 16 pseudobonds, 2685 residues, 4 models selected  

> select subtract #3

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> select subtract #1

Nothing selected  

> sequence chain #3/B

Alignment identifier is 3/B  

> select #3/B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> select add #3

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #3

Nothing selected  

> hide #!3 models

> show #!3 models

> select add #3

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select add #3

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #3

Nothing selected  

> sequence chain #3/A

Alignment identifier is 3/A  

> sequence chain #3/A

Destroying pre-existing alignment with identifier 3/A  
Alignment identifier is 3/A  

> select #3/B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> select #3/B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> select add #3

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select add #3

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select #3/B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> select #3/A:1-114

17430 atoms, 17690 bonds, 1140 residues, 1 model selected  

> run('align #0 to #1') # Align structure 0 (protein1) to structure 1
> (protein2)

Unknown command: run('align #0 to #1') # Align structure 0 (protein1) to
structure 1 (protein2)  

> color sel red

> ui tool show ""Color Actions""

> color sel cyan

> color sel forest green

> color sel lime target cspf

> color sel cyan target acspfl

> color sel lime target acspfl

> color sel yellow target acspfl

> color sel black target acspfl

> color sel lime target acspfl

> color sel yellow target acspfl

> color sel dark gray target acspfl

> color sel bynucleotide target acspfl

> color sel bychain target acspfl

> color sel bypolymer target acspfl

> color sel byhetero target acspfl

> color sel byelement target acspfl

> color sel bynucleotide target acspfl

> color sel bychain target acspfl

> color sel #e7ffe5ff target acspfl

> color sel #e7ffe4ff target acspfl

> color sel #e4ffc0ff target acspfl

> color sel #e4ff87ff target acspfl

> color sel #e2ff4eff target acspfl

> color sel #e4ff39ff target acspfl

> color sel #e9ff30ff target acspfl

> color sel #ecff2dff target acspfl

> color sel #ecff2cff target acspfl

> color sel #eeff26ff target acspfl

> color sel #f2ff20ff target acspfl

> color sel #f7ff1cff target acspfl

> color sel #faff17ff target acspfl

> color sel #fbff15ff target acspfl

> color sel #fffb1aff target acspfl

> color sel #ffea1cff target acspfl

> color sel #ffe31bff target acspfl

> color sel #ffe11aff target acspfl

> color sel #ffe019ff target acspfl

> color sel #ffdf19ff target acspfl

> color sel #ffe018ff target acspfl

> color sel #fff517ff target acspfl

> color sel #fbff13ff target acspfl

> color sel #f8ff12ff target acspfl

> color sel #f8ff11ff target acspfl

> color sel #f0ff0fff target acspfl

> color sel #e9ff0dff target acspfl

> color sel #e1ff0bff target acspfl

> color sel #d8ff08ff target acspfl

> color sel #d1ff04ff target acspfl

> color sel #d0ff04ff target acspfl

> color sel #d0ff05ff target acspfl

> color sel #d6ff09ff target acspfl

> color sel #d7ff0aff target acspfl

> color sel #d8ff0bff target acspfl

> color sel #d8ff0b00 target acspfl

> color sel #d8ff0b03 target acspfl

> color sel #d8ff0b1b target acspfl

> color sel #d8ff0b2f target acspfl

> color sel #d8ff0b43 target acspfl

> color sel #d8ff0b49 target acspfl

> color sel #d8ff0b48 target acspfl

> color sel #d8ff0b3c target acspfl

> color sel #d8ff0b2f target acspfl

> color sel #d8ff0b2d target acspfl

> color sel #d8ff0b2c target acspfl

> color sel #d8ff0b23 target acspfl

> color sel #d8ff0b1b target acspfl

> color sel #d8ff0b15 target acspfl

> color sel #d8ff0b0c target acspfl

> color sel #d8ff0b04 target acspfl

> color sel #d8ff0b00 target acspfl

> color sel #d8ff0b0a target acspfl

> color sel #d8ff0b7c target acspfl

> color sel #d8ff0bbc target acspfl

> color sel #d8ff0bc9 target acspfl

> color sel #d8ff0bd3 target acspfl

> color sel #d8ff0bde target acspfl

> color sel #d8ff0be9 target acspfl

> color sel #d8ff0bed target acspfl

> color sel #d8ff0bee target acspfl

> color sel #d8ff0bfe target acspfl

> color sel #d8ff0bff target acspfl

> color sel cornflower blue target acspfl

> color sel yellow target acspfl

> color sel lime target acspfl

> color sel bychain target acspfl

> color sel bynucleotide target acspfl

> color sel bypolymer target acspfl

> color sel byhetero target acspfl

> color sel byelement target acspfl

> color sel bynucleotide target acspfl

> color sel yellow target acspfl

> select add #3

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select add #3

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select #3/B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> select #3/A:1-114

17430 atoms, 17690 bonds, 1140 residues, 1 model selected  

> cartoon sel

No Surface models open  

> cartoon style sel modeHelix tube sides 20

> cartoon style (sel & coil) xsection oval

> cartoon style sel xsection barbell modeHelix default

> cartoon style sel xsection rectangle modeHelix default

> cartoon style (sel & coil) xsection oval

> cartoon style sel xsection barbell modeHelix default

> ui tool show ""Find Cavities""

> select coil

12157 atoms, 12241 bonds, 24 pseudobonds, 1489 residues, 6 models selected  

> select add #1

14765 atoms, 14971 bonds, 24 pseudobonds, 1802 residues, 6 models selected  

> select add #2

17373 atoms, 17701 bonds, 24 pseudobonds, 2115 residues, 6 models selected  

> select subtract #2

11337 atoms, 11519 bonds, 16 pseudobonds, 1347 residues, 4 models selected  

> select subtract #1

5301 atoms, 5337 bonds, 8 pseudobonds, 579 residues, 2 models selected  

> select helix

7278 atoms, 7336 bonds, 652 residues, 3 models selected  

> select strand

16103 atoms, 16164 bonds, 1303 residues, 3 models selected  

> select add #3

26175 atoms, 26572 bonds, 8 pseudobonds, 2245 residues, 4 models selected  

> select add #2

30861 atoms, 31404 bonds, 16 pseudobonds, 2849 residues, 5 models selected  

> select add #1

35547 atoms, 36236 bonds, 24 pseudobonds, 3453 residues, 6 models selected  

> select subtract #1

29511 atoms, 30054 bonds, 16 pseudobonds, 2685 residues, 4 models selected  

> select subtract #2

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #3

Nothing selected  

> select #3/B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> color (#!3 & sel) purple

> select add #3

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #3

Nothing selected  

> set bgColor white

> set bgColor black

> set bgColor white

> lighting full

> lighting soft

> set bgColor black

> lighting full

> lighting soft

> lighting simple

> lighting soft

> lighting full

> style #!3 ball

Changed 23475 atom styles  

> style #!3 ball

Changed 23475 atom styles  

> style #!3 sphere

Changed 23475 atom styles  

> style #!3 ball

Changed 23475 atom styles  

> style #!3 stick

Changed 23475 atom styles  

> hide #!3 cartoons

> show #!3 cartoons

> show #!3 atoms

> hide #!3 atoms

> show #!3 atoms

> hide #!3 atoms

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/mohitkwatra/Desktop/movie1.mp4

Movie saved to /Users/mohitkwatra/Desktop/movie1.mp4  
  

> color #!3 byhetero

> coulombic #!3

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
model_1.pdb #3/B GLN 282  
model_1.pdb #3/B GLN 282  
model_1.pdb #3/B GLU 353  
model_1.pdb #3/B GLU 353  
model_1.pdb #3/B ASN 356  
model_1.pdb #3/B ASN 356  
model_1.pdb #3/B PHE 381  
model_1.pdb #3/B PHE 381  
model_1.pdb #3/B GLU 382  
model_1.pdb #3/B GLU 382  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for model_1.pdb_A SES surface #3.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #3.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic #!3

Coulombic values for model_1.pdb_A SES surface #3.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #3.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> color #!3 byhetero

> color #!3 bynucleotide

> style #!3 stick

Changed 23475 atom styles  

> color #!3 bychain

> rainbow #!3

> color #!3 bypolymer

> coulombic #!3

Coulombic values for model_1.pdb_A SES surface #3.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #3.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic #!3

Coulombic values for model_1.pdb_A SES surface #3.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #3.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic #!3

Coulombic values for model_1.pdb_A SES surface #3.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #3.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> hbonds #!3 reveal true

6146 hydrogen bonds found  

> ~hbonds

> style #!3 ball

Changed 23475 atom styles  

> style #!3 sphere

Changed 23475 atom styles  

> nucleotides #!3 atoms

> style nucleic & #!3 stick

Changed 0 atom styles  

> nucleotides #!3 atoms

> style nucleic & #!3 stick

Changed 0 atom styles  

> style #!3 stick

Changed 23475 atom styles  

> set bgColor white

> set bgColor black

> style #3 stick

Changed 23475 atom styles  

> cartoon style #3 modeHelix tube sides 20

> color #!3 byhetero

> color #!3 bychain

> rainbow #!3

> coulombic #!3

Coulombic values for model_1.pdb_A SES surface #3.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #3.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> rainbow #!3

> mlp #!3

Map values for surface ""model_1.pdb_A SES surface"": minimum -188.4, mean
-13.67, maximum 123.5  
Map values for surface ""model_1.pdb_B SES surface"": minimum -29.34, mean
-5.485, maximum 22.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> color #!3 bynucleotide

> style #!3 sphere

Changed 23475 atom styles  

> style #!3 stick

Changed 23475 atom styles  

> nucleotides #!3 atoms

> style nucleic & #!3 stick

Changed 0 atom styles  

> nucleotides #!3 fill

> style nucleic & #!3 stick

Changed 0 atom styles  

> nucleotides #!3 tube/slab shape box

> nucleotides #!3 ladder

> style #!3 ball

Changed 23475 atom styles  

> color #!3 bynucleotide

> color #!3 byhetero

> color #!3 bychain

> color #!3 bypolymer

> select #3/B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> style sel ball

Changed 6036 atom styles  

> color (#!3 & sel) red

> color (#!3 & sel) magenta

> 6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected

Unknown command: 6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models
selected  

> view clip false

> log metadata #1

No models had metadata

> log chains #1

Chain information for ligand_Parkin_5c1z_l.pdb #1  
---  
Chain | Description  
B | No description available  
  

> log metadata #2

No models had metadata

> log chains #2

Chain information for ligand_Parkin_5c1z_l.pdb #2  
---  
Chain | Description  
B | No description available  
  

> log metadata #3

No models had metadata

> log chains #3

Chain information for model_1.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> close

> open
> /Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb
> format pdb

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2126.52  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 42.04  
  
Chain information for model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> close

> open
> /Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb
> format pdb

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2126.52  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 42.04  
  
Chain information for model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> coulombic

The following residues are missing heavy (non-hydrogen) atoms, which may
result in inaccurate electrostatics:  
/B GLN 282  
/B GLN 282  
/B GLU 353  
/B GLU 353  
/B ASN 356  
/B ASN 356  
/B PHE 381  
/B PHE 381  
/B GLU 382  
/B GLU 382  

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> coulombic

Coulombic values for model_1.pdb_A SES surface #1.2: minimum, -97.24, mean
-1.57, maximum 71.74  
Coulombic values for model_1.pdb_B SES surface #1.3: minimum, -32.94, mean
-0.47, maximum 17.47  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp

Map values for surface ""model_1.pdb_A SES surface"": minimum -188.4, mean
-13.67, maximum 123.5  
Map values for surface ""model_1.pdb_B SES surface"": minimum -29.34, mean
-5.485, maximum 22.41  
To also show corresponding color key, enter the above mlp command and add key
true  

> color bfactor

23475 atoms, 1917 residues, 2 surfaces, atom bfactor range 0 to 0  

> rainbow

> hbonds reveal true

5648 hydrogen bonds found  

> hbonds reveal true

5648 hydrogen bonds found  

> hbonds reveal true

5648 hydrogen bonds found  

> close

> close #

Expected a models specifier or a keyword  

> open
> /Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb
> format pdb

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2126.52  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 42.04  
  
Chain information for model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> hbonds reveal true

5648 hydrogen bonds found  

> hbonds reveal true

5648 hydrogen bonds found  

> hbonds reveal true

5648 hydrogen bonds found  

> ~hbonds

Alignment identifier is 1/A  
Alignment identifier is 1/B  

> interfaces ~solvent

1 buried areas: A B 1270  

> interfaces ~solvent

1 buried areas: A B 1270  

> interfaces ~solvent

1 buried areas: A B 1270  

> interfaces ~solvent

1 buried areas: A B 1270  

> interfaces ~solvent

1 buried areas: A B 1270  

> select /A

17439 atoms, 17690 bonds, 1149 residues, 1 model selected  

> style sel stick

Changed 17439 atom styles  

> style sel stick

Changed 17439 atom styles  

> style sel ball

Changed 17439 atom styles  

> style sel sphere

Changed 17439 atom styles  

> style sel ball

Changed 17439 atom styles  

> style sel sphere

Changed 17439 atom styles  

> select add #1

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> style sel sphere

Changed 23475 atom styles  

> style sel sphere

Changed 23475 atom styles  

> style sel stick

Changed 23475 atom styles  

> style sel ball

Changed 23475 atom styles  

> style sel ball

Changed 23475 atom styles  

> nucleotides sel ladder

> nucleotides sel atoms

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel tube/slab shape box

> nucleotides sel ladder

> style sel stick

Changed 23475 atom styles  

> style sel stick

Changed 23475 atom styles  

> style sel stick

Changed 23475 atom styles  

> style sel stick

Changed 23475 atom styles  

> style sel sphere

Changed 23475 atom styles  

> style sel ball

Changed 23475 atom styles  

> hide sel surfaces

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> hide sel atoms

> show sel atoms

> hide sel surfaces

> show sel surfaces

> hide sel surfaces

> hide sel cartoons

> show sel cartoons

> hide sel cartoons

> select subtract #1

2 models selected  

> hbonds reveal true

5648 hydrogen bonds found  

> hbonds reveal true

5648 hydrogen bonds found  

> interfaces ~solvent

1 buried areas: A B 1270  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  
Destroying pre-existing alignment with identifier 1/A  
Alignment identifier is 1/A  
Destroying pre-existing alignment with identifier 1/B  
Alignment identifier is 1/B  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> lighting soft

> lighting full

> lighting simple

> lighting flat

> lighting shadows true intensity 0.5

> lighting simple

> ui tool show ""Side View""

> view

> ui tool show ""Side View""

> view orient

> set bgColor white

> set bgColor gray

> set bgColor black

> volume style surface

No volumes specified  

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> transparency 50

> select add #1

23475 atoms, 23872 bonds, 5656 pseudobonds, 1917 residues, 3 models selected  

> volume style surface

No volumes specified  

> volume style mesh

No volumes specified  

> volume style image

No volumes specified  

> volume style image

No volumes specified  

> transparency sel 0

> volume showOutlineBox true

No volumes specified  

> volume step 1

No volumes specified  

> volume step 2

No volumes specified  

> volume planes z style image imageMode ""full region""

No volumes specified  

Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 0 maps.  

> volume appearance airways

No volumes specified  

> volume appearance airways

No volumes specified  

> volume appearance airways

No volumes specified  

> volume appearance airways

No volumes specified  

> volume appearance chest

No volumes specified  

> volume appearance chest

No volumes specified  

> show sel atoms

> hide sel atoms

> show sel atoms

> show sel cartoons

> style sel stick

Changed 23475 atom styles  

> style sel ball

Changed 23475 atom styles  

> style sel sphere

Changed 23475 atom styles  

> style sel stick

Changed 23475 atom styles  

> select subtract #1

2 models selected  

> close

> open
> /Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb
> format pdb

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2126.52  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 42.04  
  
Chain information for model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> hbonds reveal true

5648 hydrogen bonds found  

> hbonds reveal true

5648 hydrogen bonds found  

> hbonds reveal true

5648 hydrogen bonds found  

> hbonds reveal true

5648 hydrogen bonds found  

> ~hbonds

> close

> open
> /Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb
> format pdb

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2126.52  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 42.04  
  
Chain information for model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> undo

Undo failed, probably because structures have been modified.  

> select /A

17439 atoms, 17690 bonds, 1149 residues, 1 model selected  

> style sel stick

Changed 17439 atom styles  

> style sel sphere

Changed 17439 atom styles  

> style sel sphere

Changed 17439 atom styles  

> style sel stick

Changed 17439 atom styles  

> style sel ball

Changed 17439 atom styles  

> style sel ball

Changed 17439 atom styles  

> style sel sphere

Changed 17439 atom styles  

> style sel stick

Changed 17439 atom styles  

> nucleotides sel fill

> style nucleic & sel stick

Changed 0 atom styles  

> nucleotides sel ladder

> select add #1

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #1

Nothing selected  

> close

> open
> /Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb
> format pdb

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_1.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 1  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2126.52  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 42.04  
  
Chain information for model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> nucleotides atoms

> style nucleic stick

Changed 0 atom styles  

> color lime

> undo

> select /B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> select /A:1-114

17430 atoms, 17690 bonds, 1140 residues, 1 model selected  

> color sel cyan

> select add #1

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> color (#!1 & sel) purple

> undo

> select /A:1-114

17430 atoms, 17690 bonds, 1140 residues, 1 model selected  

> select /B:1-465

6036 atoms, 6182 bonds, 8 pseudobonds, 768 residues, 2 models selected  

> color (#!1 & sel) yellow

> select add #1

23475 atoms, 23872 bonds, 8 pseudobonds, 1917 residues, 2 models selected  

> select subtract #1

Nothing selected  

> lighting full

> lighting soft

> lighting simple

> lighting flat

> lighting shadows true intensity 0.5

> graphics silhouettes false

> lighting simple

> set bgColor gray

> set bgColor white

> set bgColor black

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/mohitkwatra/Desktop/movie2.mp4

Movie saved to /Users/mohitkwatra/Desktop/movie2.mp4  
  

> hbonds reveal true

5648 hydrogen bonds found  

> select /A:1-114

17430 atoms, 17690 bonds, 5000 pseudobonds, 1140 residues, 2 models selected  

> select /B:1-465

6036 atoms, 6182 bonds, 610 pseudobonds, 768 residues, 3 models selected  

> select /A:1-114

17430 atoms, 17690 bonds, 5000 pseudobonds, 1140 residues, 2 models selected  

> color (#!1 & sel) #d8ff0bfe

> color (#!1 & sel) #d8ff0be0

> color (#!1 & sel) #d8ff0bd1

> color (#!1 & sel) #d8ff0bbe

> color (#!1 & sel) #d8ff0bbc

> color (#!1 & sel) #d8ff0bb9

> color (#!1 & sel) #d8ff0bad

> color (#!1 & sel) #d8ff0ba8

> color (#!1 & sel) #d8ff0b9f

> color (#!1 & sel) #d8ff0b91

> color (#!1 & sel) #d8ff0b82

> color (#!1 & sel) #d8ff0b75

> color (#!1 & sel) #d8ff0b70

> color (#!1 & sel) #d8ff0b6c

> color (#!1 & sel) #d8ff0b60

> color (#!1 & sel) #d8ff0b52

> color (#!1 & sel) #d8ff0b49

> color (#!1 & sel) #d8ff0b43

> color (#!1 & sel) #d8ff0b3f

> color (#!1 & sel) #d8ff0b37

> color (#!1 & sel) #d8ff0b31

> color (#!1 & sel) #d8ff0b2d

> color (#!1 & sel) #d8ff0b2c

> color (#!1 & sel) #d8ff0b3a

> color (#!1 & sel) #d8ff0b49

> color (#!1 & sel) #d8ff0b5b

> color (#!1 & sel) #d8ff0b71

> color (#!1 & sel) #d8ff0b89

> color (#!1 & sel) #d8ff0ba9

> color (#!1 & sel) #d8ff0bb0

> color (#!1 & sel) #d8ff0bb5

> color (#!1 & sel) #d8ff0bcc

> color (#!1 & sel) #d8ff0bda

> color (#!1 & sel) #d8ff0bdd

> color (#!1 & sel) #d8ff0be3

> color (#!1 & sel) #d8ff0be7

> color (#!1 & sel) #d8ff0bce

> color (#!1 & sel) #d8ff0bcb

> color (#!1 & sel) #d8ff0bd2

> color (#!1 & sel) #d8ff0bef

> color (#!1 & sel) #d8ff0bf8

> color (#!1 & sel) #d8ff0bff

> color (#!1 & sel) #d2ff04ff

> color (#!1 & sel) #d6ff0dff

> color (#!1 & sel) #abff48ff

> color (#!1 & sel) #80ff4eff

> color (#!1 & sel) #5cff44ff

> color (#!1 & sel) #42ff3cff

> color (#!1 & sel) #3dff3aff

> color (#!1 & sel) #39ff3eff

> color (#!1 & sel) #3aff46ff

> color (#!1 & sel) #3bff47ff

> color (#!1 & sel) #4dff66ff

> color (#!1 & sel) #56ff75ff

> color (#!1 & sel) #56ff76ff

> color (#!1 & sel) #59ff7bff

> color (#!1 & sel) #63ff8bff

> color (#!1 & sel) #6cff93ff

> color (#!1 & sel) #6dff94ff

> color (#!1 & sel) #7dff95ff

> color (#!1 & sel) #89ff9dff

> color (#!1 & sel) #90ffa0ff

> color (#!1 & sel) #8fff9fff

> color (#!1 & sel) #79ff94ff

> color (#!1 & sel) #72ff90ff

> color (#!1 & sel) #72ff90fe

> color (#!1 & sel) #72ff90f1

> color (#!1 & sel) #72ff90e9

> color (#!1 & sel) #72ff90e5

> color (#!1 & sel) #72ff90d6

> color (#!1 & sel) #72ff90ca

> color (#!1 & sel) #72ff90c9

> color (#!1 & sel) #72ff90ba

> color (#!1 & sel) #72ff90b1

> color (#!1 & sel) #72ff90b0

> color (#!1 & sel) #72ff90a8

> color (#!1 & sel) #72ff90a7

> select add #1

23475 atoms, 23872 bonds, 5656 pseudobonds, 1917 residues, 3 models selected  

> select subtract #1

Nothing selected  

> color #dadadaa7

> color #d9d9d9a7

> color #d6d6d6a7

> color #cececea7

> color #c6c6c6a7

> color #bdbdbda7

> color #bababaa7

> color #b7b7b7a7

> color #b6b6b6a7

> color #b4b4b4a7

> color #b1b1b1a7

> color #afafafa7

> color #aeaeaea7

> color #acacaca7

> color #aaaaaaa7

> color #a9a9a9a7

> color #a8a8a8a7

> color #a5a5a5a7

> color #a1a1a1a7

> color #9f9f9fa7

> color #9e9e9ea7

> color #9d9d9da7

> color #9c9c9ca7

> color #9b9b9ba7

> color #9a9a9aa7

> color #999999a7

> color #989898a7

> color #979797a7

> color #969696a7

> color #949494a7

> color #929292a7

> color #909090a7

> color #8d8d8da7

> color #8b8b8ba7

> color #898989a7

> color #868686a7

> color #848484a7

> color #818181a7

> color #7e7e7ea7

> color #7b7b7ba7

> color #767676a7

> color #717171a7

> color #6d6d6da7

> color #6b6b6ba7

> color #696969a7

> color #676767a7

> color #666666a7

> color #636363a7

> color #626262a7

> color #616161a7

> color #626262a7

> color #6c6c6ca7

> color #767676a7

> color #818181a7

> color #8a8a8aa7

> color #969696a7

> color #a2a2a2a7

> color #acacaca7

> color #b2b2b2a7

> color #b7b7b7a7

> color #b9b9b9a7

> color #bdbdbda7

> color #c0c0c0a7

> color #c2c2c2a7

> color #c3c3c3a7

> color #c4c4c4a7

> color #c5c5c5a7

> select /B:1-465

6036 atoms, 6182 bonds, 610 pseudobonds, 768 residues, 3 models selected  

> color (#!1 & sel) #74fae9ff

> color (#!1 & sel) #75fb5cff

> color (#!1 & sel) #74fa55ff

> color (#!1 & sel) #75fb4dff

> color (#!1 & sel) #76fb4cff

> color (#!1 & sel) #7ffb4cff

> color (#!1 & sel) #8efc4dff

> color (#!1 & sel) #94fc4dff

> color (#!1 & sel) #9cfc4eff

> color (#!1 & sel) #a8fc4eff

> color (#!1 & sel) #b2fc4fff

> color (#!1 & sel) #bdfc4fff

> color (#!1 & sel) #c4fc50ff

> color (#!1 & sel) #bfbfbfff

> color (#!1 & sel) #808080ff

> color (#!1 & sel) #5d5d5dff

> color (#!1 & sel) #706f70ff

> color (#!1 & sel) #707067ff

> color (#!1 & sel) #706e59ff

> color (#!1 & sel) #706c4cff

> color (#!1 & sel) #706b42ff

> color (#!1 & sel) #706a3bff

> color (#!1 & sel) #706a36ff

> color (#!1 & sel) #70692fff

> color (#!1 & sel) #70692aff

> color (#!1 & sel) #706929ff

> color (#!1 & sel) #706a24ff

> color (#!1 & sel) #70691aff

> color (#!1 & sel) #706818ff

> color (#!1 & sel) #545454ff

> color (#!1 & sel) #555555ff

> color (#!1 & sel) #838383ff

> color (#!1 & sel) #c1c1c1ff

> color (#!1 & sel) #dcdcdcff

> color (#!1 & sel) #e1e1e1ff

> color (#!1 & sel) #e3e3e3ff

> color (#!1 & sel) #e6e6e6ff

> color (#!1 & sel) #e8e8e8ff

> color (#!1 & sel) #e9e9e9ff

> color (#!1 & sel) #e8e8e8ff

> color (#!1 & sel) #e3e3e3ff

> color (#!1 & sel) #e0e0e0ff

> color (#!1 & sel) #dfdfdfff

> color (#!1 & sel) #d7d7d7ff

> color (#!1 & sel) #cdcdcdff

> color (#!1 & sel) #cbcbcbff

> color (#!1 & sel) #00f900ff

> color (#!1 & sel) #00fdffff

> color (#!1 & sel) #0433ffff

> color (#!1 & sel) #fffb00ff

> color (#!1 & sel) #ff9300ff

> select /A:1-114

17430 atoms, 17690 bonds, 5000 pseudobonds, 1140 residues, 2 models selected  

> color (#!1 & sel) #fffb00ff

> color (#!1 & sel) #8efa00ff

> color (#!1 & sel) #d4fb79ff

> color (#!1 & sel) #d4fb79ef

> color (#!1 & sel) #d4fb79eb

> color (#!1 & sel) #d4fb79e0

> color (#!1 & sel) #d4fb79d5

> color (#!1 & sel) #d4fb79cd

> color (#!1 & sel) #d4fb79cb

> color (#!1 & sel) #d4fb79b7

> color (#!1 & sel) #d4fb79b0

> color (#!1 & sel) #d4fb79af

> color (#!1 & sel) #bafc4fff

> color (#!1 & sel) #d3fd51ff

> color (#!1 & sel) #d5fd51ff

> color (#!1 & sel) #f0fd53ff

> color (#!1 & sel) #ecfd53ff

> color (#!1 & sel) #d0fd51ff

> color (#!1 & sel) #b4fc4fff

> color (#!1 & sel) #aafb4eff

> color (#!1 & sel) #94fb4dff

> color (#!1 & sel) #8bfb4dff

> color (#!1 & sel) #8cfb4dff

> color (#!1 & sel) #89fb4dff

> color (#!1 & sel) #88fb4dff

> select add #1

23475 atoms, 23872 bonds, 5656 pseudobonds, 1917 residues, 3 models selected  

> select subtract #1

Nothing selected  

> ~hbonds

> hbonds reveal true

5648 hydrogen bonds found  

> color byhetero

> color bychain

> color bypolymer

> color byhetero

> style sphere

Changed 23475 atom styles  

> style sphere

Changed 23475 atom styles  

> style stick

Changed 23475 atom styles  

> undo

> save ""/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
> (1)/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/Model 1.gif""
> width 1344 height 903 supersample 3

> run('movie record') # Start recording the movie

Unknown command: run('movie record') # Start recording the movie  

> run('turn x 10') # Example: Rotate by 10 degrees around the X-axis

Unknown command: run('turn x 10') # Example: Rotate by 10 degrees around the
X-axis  

> run('movie stop') # Stop recording the movie

Unknown command: run('movie stop') # Stop recording the movie  

> run('movie save animation.gif') # Save the recorded animation as a GIF

Unknown command: run('movie save animation.gif') # Save the recorded animation
as a GIF  

> run('movie record') # Start recording the movie

Unknown command: run('movie record') # Start recording the movie  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/mohitkwatra/Desktop/movie3.mp4

Movie saved to /Users/mohitkwatra/Desktop/movie3.mp4  
  

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/mohitkwatra/Desktop/movie4.mp4

Movie saved to /Users/mohitkwatra/Desktop/movie4.mp4  
  

> save my_animation.gif

Unknown command: movie save my_animation.gif  

> set bgColor white

> movie record

> turn y 2 180

> wait 180

> movie encode /Users/mohitkwatra/Desktop/movie1.mp4

Movie saved to /Users/mohitkwatra/Desktop/movie1.mp4  
  

> show target m

> log metadata #1

No models had metadata

> log chains #1

Chain information for model_1.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
  

> open ""/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
> (1)/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_2.pdb""

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
(1)/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_2.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 2  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2007.38  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 66.14  
  
Chain information for model_2.pdb #2  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> open ""/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
> (1)/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_2.pdb""

Summary of feedback from opening
/Users/mohitkwatra/Downloads/USP13_parkin_Zn_hdock
(1)/multi_lig_out/ligand_Parkin_5c1z_l_receptor_Zn_USP_2l80_r/model_2.pdb  
---  
warnings | Ignored bad PDB record found on line 1  
REMARK Number: 2  
  
Ignored bad PDB record found on line 2  
REMARK Ligand: ligand_Parkin_5c1z_l.pdb  
  
Ignored bad PDB record found on line 3  
REMARK Contact: 0 0 0  
  
Ignored bad PDB record found on line 4  
REMARK Score: -2007.38  
  
Ignored bad PDB record found on line 5  
REMARK RMSD: 66.14  
  
Chain information for model_2.pdb #3  
---  
Chain | Description  
A | No description available  
B | No description available  
  
144 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.  
Computing secondary structure  

> hide #!3 models

> hide #!1 models

> show #!1 models

> hide #!1 models

> hbonds #!2 reveal true

27082 hydrogen bonds found  

> hide #4 models

> show #4 models

> hide #!2 models

> show #!3 models

> hide #4 models

> hide #!3 models

> show #!1 models

> hbonds #!1 reveal true

26044 hydrogen bonds found  

> show #4 models

> hide #4 models

> show #!3 models

> hide #!1 models

> hide #!3 models

> show #!2 models

> show #4 models

> hide #4 models

> show #4 models

> hide #4 models

> ~hbonds

> undo

> hide #!1 models

> show #!2 models

> ~hbonds

> hbonds #!2 reveal true

27082 hydrogen bonds found  

> color #2,4 #00f900ff


===== Log before crash end =====

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.9 (2024-12-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2
OpenGL vendor: Apple

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: Mac14,7
      Model Number: MNEQ3LL/A
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 8 GB
      System Firmware Version: 10151.140.19
      OS Loader Version: 10151.140.19

Software:

    System Software Overview:

      System Version: macOS 14.6.1 (23G93)
      Kernel Version: Darwin 23.6.0
      Time since boot: 20 hours, 38 minutes

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Support: Metal 3
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Mirror: On
          Mirror Status: Hardware Mirror
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal
        Mohit's TV:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Framebuffer Depth: 24-Bit Color (ARGB8888)
          Main Display: Yes
          Mirror: On
          Mirror Status: Master Mirror
          Connection Type: AirPlay
          Virtual Device: Yes


Installed Packages:
    alabaster: 1.0.0
    anyio: 4.7.0
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 3.0.0
    auditwheel: 6.1.0
    babel: 2.16.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 3.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.4.post1
    charset-normalizer: 3.4.0
    ChimeraX-AddCharge: 1.5.18
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.16.1
    ChimeraX-AlphaFold: 1.0.1
    ChimeraX-AltlocExplorer: 1.1.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58.8
    ChimeraX-AtomicLibrary: 14.1.11
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 3.0.0
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.13.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.4.0
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.3
    ChimeraX-ColorActions: 1.0.5
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.4
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.6
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.4.1
    ChimeraX-Hbonds: 2.5
    ChimeraX-Help: 1.3
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.3
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-KVFinder: 1.2.1
    ChimeraX-Label: 1.1.14
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.3
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.6
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7.2
    ChimeraX-MedicalToolbar: 1.1
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.2
    ChimeraX-MMTF: 2.2
    ChimeraX-ModelArchive: 1.0
    ChimeraX-Modeller: 1.5.18
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-MutationScores: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.2
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.2
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.14
    ChimeraX-OrthoPick: 1.0.1
    ChimeraX-PDB: 2.7.6
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.4
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1.2
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.6.2
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.3.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-Segmentations: 3.5.6
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.14
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.2.0
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-SimilarStructures: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.18.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.2.3
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.41
    ChimeraX-Umap: 1.0
    ChimeraX-uniprot: 2.3.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.3.1
    cxservices: 1.2.3
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.9
    decorator: 5.1.1
    docutils: 0.21.2
    executing: 2.1.0
    filelock: 3.15.4
    fonttools: 4.55.3
    funcparserlib: 2.0.0a0
    glfw: 2.8.0
    grako: 3.16.5
    h11: 0.14.0
    h5py: 3.12.1
    html2text: 2024.2.26
    httpcore: 1.0.7
    httpx: 0.28.1
    idna: 3.10
    ihm: 1.3
    imagecodecs: 2024.6.1
    imagesize: 1.4.1
    ipykernel: 6.29.5
    ipython: 8.26.0
    ipywidgets: 8.1.5
    jedi: 0.19.1
    Jinja2: 3.1.4
    jupyter_client: 8.6.2
    jupyter_core: 5.7.2
    jupyterlab_widgets: 3.0.13
    kiwisolver: 1.4.7
    line_profiler: 4.1.3
    lxml: 5.2.2
    lz4: 4.3.3
    MarkupSafe: 3.0.2
    matplotlib: 3.9.2
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    ndindex: 1.9.2
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.2
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.4.0
    pip: 24.2
    pkginfo: 1.11.1
    platformdirs: 4.3.6
    prompt_toolkit: 3.0.48
    psutil: 6.0.0
    ptyprocess: 0.7.0
    pure_eval: 0.2.3
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pyelftools: 0.31
    Pygments: 2.18.0
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.2.0
    pyproject_hooks: 1.2.0
    PyQt6-commercial: 6.7.1
    PyQt6-Qt6: 6.7.3
    PyQt6-WebEngine-commercial: 6.7.0
    PyQt6-WebEngine-Qt6: 6.7.3
    PyQt6-WebEngineSubwheel-Qt6: 6.7.3
    PyQt6_sip: 13.8.0
    python-dateutil: 2.9.0.post0
    pytz: 2024.2
    pyzmq: 26.2.0
    qtconsole: 5.5.2
    QtPy: 2.4.2
    qtshim: 1.0
    RandomWords: 0.4.0
    requests: 2.32.3
    scipy: 1.14.0
    setuptools: 72.1.0
    sfftk-rw: 0.8.1
    six: 1.16.0
    sniffio: 1.3.1
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.6
    Sphinx: 8.0.2
    sphinx-autodoc-typehints: 2.2.3
    sphinxcontrib-applehelp: 2.0.0
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 2.0.0
    sphinxcontrib-htmlhelp: 2.1.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 2.0.0
    sphinxcontrib-serializinghtml: 2.0.0
    stack-data: 0.6.3
    superqt: 0.6.3
    tables: 3.10.1
    tcia_utils: 1.5.1
    tifffile: 2024.7.24
    tinyarray: 1.2.4
    tornado: 6.4.2
    traitlets: 5.14.3
    typing_extensions: 4.12.2
    tzdata: 2024.2
    urllib3: 2.2.3
    wcwidth: 0.2.13
    webcolors: 24.6.0
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.13
}}}
"	defect	closed	normal		Window Toolkit		duplicate						all	ChimeraX