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Opened 19 months ago
Closed 19 months ago
#14839 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.1.1-x86_64-i386-64bit
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff84de0cb40 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 721 in restore
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/session.py", line 1017 in open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py", line 37 in open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.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-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334 in _qt_safe
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, chimerax.surface._surface, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.pdb._pdbio, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, pandas._libs.tslibs.ccalendar, pandas._libs.tslibs.np_datetime, pandas._libs.tslibs.dtypes, pandas._libs.tslibs.base, pandas._libs.tslibs.nattype, pandas._libs.tslibs.timezones, pandas._libs.tslibs.fields, pandas._libs.tslibs.timedeltas, pandas._libs.tslibs.tzconversion, pandas._libs.tslibs.timestamps, pandas._libs.properties, pandas._libs.tslibs.offsets, pandas._libs.tslibs.strptime, pandas._libs.tslibs.parsing, pandas._libs.tslibs.conversion, pandas._libs.tslibs.period, pandas._libs.tslibs.vectorized, pandas._libs.ops_dispatch, pandas._libs.missing, pandas._libs.hashtable, pandas._libs.algos, pandas._libs.interval, pandas._libs.lib, pandas._libs.ops, numexpr.interpreter, pandas._libs.hashing, pandas._libs.arrays, pandas._libs.tslib, pandas._libs.sparse, pandas._libs.internals, pandas._libs.indexing, pandas._libs.index, pandas._libs.writers, pandas._libs.join, pandas._libs.window.aggregations, pandas._libs.window.indexers, pandas._libs.reshape, pandas._libs.groupby, pandas._libs.json, pandas._libs.parsers, pandas._libs.testing, scipy._lib._ccallback_c, scipy.sparse._sparsetools, _csparsetools, scipy.sparse._csparsetools, scipy.sparse.linalg._isolve._iterative, 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.linalg._flinalg, scipy.sparse.linalg._dsolve._superlu, scipy.sparse.linalg._eigen.arpack._arpack, 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._minpack2, scipy.optimize._group_columns, scipy._lib.messagestream, scipy.optimize._trlib._trlib, numpy.linalg.lapack_lite, 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.__nnls, 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, scipy.ndimage._nd_image, _ni_label, scipy.ndimage._ni_label, scipy.integrate._odepack, scipy.integrate._quadpack, scipy.integrate._vode, scipy.integrate._dop, scipy.integrate._lsoda, scipy.special.cython_special, scipy.stats._stats, scipy.stats.beta_ufunc, scipy.stats._boost.beta_ufunc, scipy.stats.binom_ufunc, scipy.stats._boost.binom_ufunc, scipy.stats.nbinom_ufunc, scipy.stats._boost.nbinom_ufunc, scipy.stats.hypergeom_ufunc, scipy.stats._boost.hypergeom_ufunc, scipy.stats.ncf_ufunc, scipy.stats._boost.ncf_ufunc, scipy.stats.ncx2_ufunc, scipy.stats._boost.ncx2_ufunc, scipy.stats.nct_ufunc, scipy.stats._boost.nct_ufunc, scipy.stats.skewnorm_ufunc, scipy.stats._boost.skewnorm_ufunc, scipy.stats.invgauss_ufunc, scipy.stats._boost.invgauss_ufunc, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, scipy.stats._biasedurn, scipy.stats._levy_stable.levyst, scipy.stats._stats_pythran, scipy._lib._uarray._uarray, scipy.stats._statlib, scipy.stats._sobol, scipy.stats._qmc_cy, scipy.stats._mvn, scipy.stats._rcont.rcont, scipy.cluster._vq, scipy.cluster._hierarchy, scipy.cluster._optimal_leaf_ordering, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize (total: 202)
{"app_name":"ChimeraX","timestamp":"2024-03-28 11:52:16.00 +1100","app_version":"1.7.0","slice_uuid":"194a3167-3db5-3029-8d22-1d742b826bb9","build_version":"1.7.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.1.1 (23B81)","roots_installed":0,"name":"ChimeraX","incident_id":"BDC2A6F3-FB1E-4CC1-9A22-14AA86B0A452"}
{
"uptime" : 780000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 4160,
"deployVersion" : 210,
"modelCode" : "iMac20,1",
"coalitionID" : 677,
"osVersion" : {
"train" : "macOS 14.1.1",
"build" : "23B81",
"releaseType" : "User"
},
"captureTime" : "2024-03-28 11:52:02.2192 +1100",
"codeSigningMonitor" : 0,
"incident" : "BDC2A6F3-FB1E-4CC1-9A22-14AA86B0A452",
"pid" : 36940,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-03-27 11:18:48.5591 +1100",
"procStartAbsTime" : 695359086408489,
"procExitAbsTime" : 783749873782506,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.7.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.7.0","CFBundleVersion":"1.7.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"BBE09053-ACC7-5F65-9254-4457FEC4D638","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "B9F051C4-D122-AE30-512C-FEBAD4D6B2C8",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"bridgeVersion" : {"build":"21P1069","train":"8.1"},
"sip" : "enabled",
"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737487167319\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffede000-7fffffedf000 [ 4K] r-x\/r-x SM=SHM ",
"exception" : {"codes":"0x0000000000000001, 0x00000000000000a9","rawCodes":[1,169],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x00000000000000a9"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":36940},
"ktriageinfo" : "VM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\nVM - (arg = 0x3) mach_vm_allocate_kernel failed within call to vm_map_enter\n",
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737487167319\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffede000-7fffffedf000 [ 4K] r-x\/r-x SM=SHM ",
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"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/alphafold_MORC2dimer/relaxed_model_1_multimer_v3_pred_2.pdb
Chain information for relaxed_model_1_multimer_v3_pred_2.pdb #1
---
Chain | Description
A B | No description available
> set bgColor white
> color /B hot pink
> color /A cornflower blue
> select :899-1068
5396 atoms, 5446 bonds, 340 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> select up
6746 atoms, 6810 bonds, 434 residues, 1 model selected
> select up
34268 atoms, 34612 bonds, 2136 residues, 1 model selected
> select :605-783
5668 atoms, 5730 bonds, 358 residues, 1 model selected
> hide sel cartoons
> show sel cartoons
> ui tool show XMAS
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS.csv
Unique peptide pairs: 29 out of 31
Unique peptide pairs with pseudobonds: 29
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS.csv
Unique peptide pairs: 25 out of 26
Unique peptide pairs with pseudobonds: 25
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS.csv
Unique peptide pairs: 20 out of 21
Unique peptide pairs with pseudobonds: 20
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS.csv
Unique peptide pairs: 24 out of 24
Unique peptide pairs with pseudobonds: 24
/Users/shakeel.s/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/XMAS/info_file.py:46: FutureWarning: The behavior of
DataFrame concatenation with empty or all-NA entries is deprecated. In a
future version, this will no longer exclude empty or all-NA columns when
determining the result dtypes. To retain the old behavior, exclude the
relevant entries before the concat operation.
self.df = pd.concat([self.df, df_add], ignore_index=True)
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.tsv
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsApo_20A.pb
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsApo_20A.pb
> hide #5 models
> hide #4 models
> hide #3 models
> hide #2 models
> hide #6 models
> close session
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/alphafold_MORC2dimer/relaxed_model_1_multimer_v3_pred_2.pdb
Chain information for relaxed_model_1_multimer_v3_pred_2.pdb #1
---
Chain | Description
A B | No description available
> color /B hot pink
> color /A cornflower blue
> ui tool show XMAS
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS.csv
Unique peptide pairs: 29 out of 31
Unique peptide pairs with pseudobonds: 29
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS.csv
Unique peptide pairs: 25 out of 26
Unique peptide pairs with pseudobonds: 25
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS.csv
Unique peptide pairs: 20 out of 21
Unique peptide pairs with pseudobonds: 20
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS.csv
Unique peptide pairs: 24 out of 24
Unique peptide pairs with pseudobonds: 24
/Users/shakeel.s/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/XMAS/info_file.py:46: FutureWarning: The behavior of
DataFrame concatenation with empty or all-NA entries is deprecated. In a
future version, this will no longer exclude empty or all-NA columns when
determining the result dtypes. To retain the old behavior, exclude the
relevant entries before the concat operation.
self.df = pd.concat([self.df, df_add], ignore_index=True)
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.tsv
> hide #5 models
> hide #4 models
> hide #3 models
Please select pseudobonds
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsDNA_20A.pb
> hide #2 models
> hide #6 models
> show #4 models
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAPOinAMPvsAPO_20A.pb
> hide #7 models
> hide #4 models
> color #4 #8efa00ff models
> show #4 models
> hide #4 models
> color #7 #8efa00ff models
> select subtract #4
Nothing selected
> show #7 models
> hide #7 models
> show #3 models
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsDNA_20A.pb
> close session
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/alphafold_MORC2dimer/relaxed_model_1_multimer_v3_pred_2.pdb
> format pdb
Chain information for relaxed_model_1_multimer_v3_pred_2.pdb #1
---
Chain | Description
A B | No description available
> color /A cornflower blue
> color /B hot pink
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS.csv
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS.csv
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS.csv
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS.csv
Unrecognized file suffix '.csv'
> ui tool show XMAS
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS.csv
Unique peptide pairs: 29 out of 31
Unique peptide pairs with pseudobonds: 29
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvapo_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS.csv
Unique peptide pairs: 25 out of 26
Unique peptide pairs with pseudobonds: 25
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/ampvdna_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS.csv
Unique peptide pairs: 20 out of 21
Unique peptide pairs with pseudobonds: 20
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/apo_XMAS_1.tsv
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS.csv
Unique peptide pairs: 24 out of 24
Unique peptide pairs with pseudobonds: 24
/Users/shakeel.s/Library/Application Support/ChimeraX/1.7/lib/python/site-
packages/chimerax/XMAS/info_file.py:46: FutureWarning: The behavior of
DataFrame concatenation with empty or all-NA entries is deprecated. In a
future version, this will no longer exclude empty or all-NA columns when
determining the result dtypes. To retain the old behavior, exclude the
relevant entries before the concat operation.
self.df = pd.concat([self.df, df_add], ignore_index=True)
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/DNA_XMAS_1.tsv
> hide #3 models
> hide #4 models
> hide #5 models
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsAPO_20A.pb
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAMPinAMPvsDNA_20A.pb
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedAPOinAMPvsAPO_20A.pb
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/EnrichedDNAinAMPvsDNA_20A.pb
> color #8 #8efa00ff models
> color #9 #8efa00ff models
> hide #7 models
> hide #9 models
> hide #2 models
> hide #6 models
> hide #8 models
> show #6 models
> show #7 models
> hide #7 models
> show #8 models
> hide #6 models
> hide #8 models
> show #6 models
> show #8 models
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/P4383_apo.csv
Unique peptide pairs: 286 out of 359
Unique peptide pairs with pseudobonds: 260
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/P4383_apo_1.pb
Mapping information is stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/P4383_apo_1.tsv
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/Apo_chain_interlinks_25A.pb
> hide #10 models
> hide #8 models
> hide #6 models
> show #10 models
> hide #11 models
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/Apo_chain_interlinks_25A.pb
> hide #10 models
Pseudobonds are stored in
/Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/Apo_chain_interlinks_20A.pb
> hide #12 models
> select ~sel & ##selected
892 pseudobonds, 1 model selected
> hide #13 models
> show #6 models
> show #8 models
> select subtract #10
Nothing selected
> color :82-103 white
> hide #8 models
> hide #6 models
> show #9 models
> show #7 models
> hide #9 models
> hide #7 models
> color :67-109 red
> color :82-103 white
> color /A cornflower blue
> color /B hot pink
> color :81-109 red
> show #9 models
> show #7 models
> color #7 #fffc79ff models
> color #7 #ffd479ff models
> color #7 #fffb00ff models
> color #9 #8efa00ff models
> color :495-545 dark red
> color /A steelblue
> color /B mercury
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /A steelblue
> color /B snow
> color /A steelblue
> color /A iron
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /B darkred white
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color /A lead
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color /A fern
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color #10 #5e5e5eff models
> select /A
17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected
> color (#1 & sel) gray
> color :495-545 dark red
> color :67-109 red
> color /B snow
> select /A
17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected
> color /A grey
> color :495-545 dark red
> color :81-109 red
> color :266-494 magenta
> color #9 #8efa00ff models
> color #7 #8efa00ff models
> color #7 #fffb00ff models
> color :547-584 cyan
> hide #9 models
> hide #7 models
> show #7 models
> color #7 #8efa00ff models
> color #7 #fffb00ff models
> color #7 #8efa00ff models
> color #7 #fffb00ff models
> color #9 #0096ffff models
> color #9 #8efa00ff models
> show #9 models
> color :786-851 ff7f00
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms',
'fromcartoons', 'fromribbons', or 'random' or a keyword
> color :786-851 #ff7f00
> color :966-1016 #cf597e
> color :903-1016 #cf597e
> color #9 #00f900ff models
> color #9 #8efa00ff models
> color #7 #8efa00ff models
> color #7 #fffb00ff models
> color :741-761 blue
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_1_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_1_multimer_v3_pred_0.pdb #14
---
Chain | Description
B C D | No description available
E | No description available
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_2_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_2_multimer_v3_pred_0.pdb #15
---
Chain | Description
B C D | No description available
E | No description available
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_3_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_3_multimer_v3_pred_0.pdb #16
---
Chain | Description
B C D | No description available
E | No description available
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_4_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_4_multimer_v3_pred_0.pdb #17
---
Chain | Description
B C D | No description available
E | No description available
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_5_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_5_multimer_v3_pred_0.pdb #18
---
Chain | Description
B C D | No description available
E | No description available
> hide #1 models
> hide #7 models
> hide #9 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> color bychain #14-18
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color #14-18 bychain
> hide #14 models
> show #15 models
> hide #15 models
> show #16 models
> hide #16 models
> show #17 models
> hide #17 models
> show #18 models
> select down
17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected
> select down
17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected
> select down
17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected
> close #14-18
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_1_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_1_multimer_v3_pred_0.pdb #14
---
Chain | Description
B C D | No description available
E | No description available
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_2_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_2_multimer_v3_pred_0.pdb #15
---
Chain | Description
B C D | No description available
E | No description available
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_3_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_3_multimer_v3_pred_0.pdb #16
---
Chain | Description
B C D | No description available
E | No description available
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_4_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_4_multimer_v3_pred_0.pdb #17
---
Chain | Description
B C D | No description available
E | No description available
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/XiaominProject/Neuropilin_project/alphafold/alphafold_OmiSpike_NRP1/Omi_NRP/unrelaxed_model_5_multimer_v3_pred_0.pdb
Chain information for unrelaxed_model_5_multimer_v3_pred_0.pdb #18
---
Chain | Description
B C D | No description available
E | No description available
> hide #14 models
> hide #15 models
> hide #16 models
> hide #17 models
> hide #18 models
> show #14 models
> color #14-18 bychain
> show #15 models
> hide #14 models
> hide #15 models
> show #16 models
> hide #16 models
> show #17 models
> hide #17 models
> show #18 models
> toolshed show
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 195 out of 549
Unique peptide pairs with pseudobonds: 149
Pseudobonds are stored in
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_14.pb
Mapping information is stored in
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_14.tsv
> select add #19
17134 atoms, 17306 bonds, 794 pseudobonds, 1068 residues, 11 models selected
> hide #19 models
> select subtract #19
17134 atoms, 17306 bonds, 367 pseudobonds, 1068 residues, 10 models selected
> show #19 models
> show #14 models
> hide #18 models
> hide #19 models
Pseudobonds are stored in /Users/shakeel.s/Downloads/spikenrp1_model1.pb
> hide #14 models
> show #15 models
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 195 out of 549
Unique peptide pairs with pseudobonds: 149
Pseudobonds are stored in
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_15.pb
Mapping information is stored in
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_15.tsv
Pseudobonds are stored in /Users/shakeel.s/Downloads/spikenrp1_model2.pb
> hide #21 models
> hide #20 models
> hide #22 models
> show #21 models
> hide #15 models
> show #14 models
> hide #21 models
> show #20 models
> hide #20 models
> hide #14 models
> show #16 models
Peptide pair mapping of Xi evidence file:
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5.csv
Unique peptide pairs: 195 out of 549
Unique peptide pairs with pseudobonds: 149
Pseudobonds are stored in
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_16.pb
Mapping information is stored in
/Users/shakeel.s/Downloads/P4699_Xi1.7.6.7_CSM_xiFDR2.1.5.5_16.tsv
Pseudobonds are stored in /Users/shakeel.s/Downloads/spikenrp1_model3.pb
> hide #23 models
> show #20 models
> hide #24 models
> hide #20 models
> show #14 models
> hide #16 models
> ui tool show "Show Sequence Viewer"
> sequence chain #14/B #14/C #14/D #15/B #15/C #15/D #16/B #16/C #16/D #17/B
> #17/C #17/D #18/B #18/C #18/D
Alignment identifier is 1
> select #14/B-D:841 #15/B-D:841 #16/B-D:841 #17/B-D:841 #18/B-D:841
120 atoms, 105 bonds, 15 residues, 5 models selected
> select #14/B-D:841-927 #15/B-D:841-927 #16/B-D:841-927 #17/B-D:841-927
> #18/B-D:841-927
9945 atoms, 10155 bonds, 1305 residues, 5 models selected
1 [ID: 1] region 15 chains [841-927] RMSD: 63.226
> select down
9945 atoms, 10155 bonds, 1305 residues, 5 models selected
> select down
9945 atoms, 10155 bonds, 1305 residues, 5 models selected
> select down
9945 atoms, 10155 bonds, 1305 residues, 5 models selected
> select down
9945 atoms, 10155 bonds, 1305 residues, 5 models selected
> select down
9945 atoms, 10155 bonds, 1305 residues, 5 models selected
> close #14
> close #15
> close #16
> close #17
> close #18
> close #19
> close #20
> close #21
> close #22
> close #23
> close #24
> show #1 models
> close session
> open
> /Users/shakeel.s/Documents/WEHI/Shakeel_Laboratories/MORC2/CLMS/CLMS_analysis.cxs
===== Log before crash end =====
Log:
Startup Messages
---
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle
UCSF ChimeraX version: 1.7 (2023-12-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-5.1.35
OpenGL renderer: AMD Radeon Pro 5300 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.
Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: iMac
Model Identifier: iMac20,1
Processor Name: 6-Core Intel Core i5
Processor Speed: 3.3 GHz
Number of Processors: 1
Total Number of Cores: 6
L2 Cache (per Core): 256 KB
L3 Cache: 12 MB
Hyper-Threading Technology: Enabled
Memory: 16 GB
System Firmware Version: 2020.41.1.0.0 (iBridge: 21.16.1069.0.0,0)
OS Loader Version: 580~743
Software:
System Software Overview:
System Version: macOS 14.1.1 (23B81)
Kernel Version: Darwin 23.1.0
Time since boot: 9 days, 1 hour, 43 minutes
Graphics/Displays:
AMD Radeon Pro 5300:
Chipset Model: AMD Radeon Pro 5300
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0047
ROM Revision: 113-D3220I-231
VBIOS Version: 113-D322A1XL-012
Option ROM Version: 113-D322A1XL-012
EFI Driver Version: 01.01.231
Metal Support: Metal 3
Displays:
iMac:
Display Type: Built-In Retina LCD
Resolution: Retina 5K (5120 x 2880)
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.1
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.3
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.13
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.3
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.2
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-XMAS: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.0
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
et-xmlfile: 1.1.0
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.0
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.5.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.3
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.8
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openpyxl: 3.1.2
openvr: 1.23.701
packaging: 21.3
pandas: 2.2.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
Pillow: 10.0.1
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
QtRangeSlider: 0.1.5
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
seaborn: 0.13.2
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.7
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.5
sphinxcontrib-htmlhelp: 2.0.4
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.6
sphinxcontrib-serializinghtml: 1.1.9
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.3
urllib3: 2.1.0
wcwidth: 0.2.12
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 19 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Core |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Crash in garbage collection |
comment:2 by , 19 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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Hi Shabih,
--Eric