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Opened 17 months ago
Closed 17 months ago
#15359 closed defect (duplicate)
Crash in garbage collection
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-13.4.1-x86_64-i386-64bit
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault
Current thread 0x00007ff845189640 (most recent call first):
Garbage-collecting
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/serialize.py", line 81 in msgpack_deserialize
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 514 in collated_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2908 in run
File "/Applications/ChimeraX-1.7.1.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-1.7.1.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-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, openmm._openmm, openmm.app.internal.compiled, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, scipy._lib._ccallback_c, scipy.special._ufuncs_cxx, scipy.special._ufuncs, scipy.special._specfun, scipy.special._comb, 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._isolve._iterative, 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.linalg._flinalg, scipy.special._ellip_harm_2, scipy.interpolate._fitpack, scipy.interpolate.dfitpack, 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.spatial.transform._rotation, scipy.optimize._direct, scipy.interpolate._bspl, scipy.interpolate._ppoly, scipy.interpolate.interpnd, scipy.interpolate._rbfinterp_pythran, scipy.interpolate._rgi_cython, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.mmcif.mmcif_write, PIL._imagingmath, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, lxml._elementpath, lxml.etree, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 132)
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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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open /Users/johncowgill/Desktop/a5b3/ApoLMNG/Autosharpen_1/Apo.ccp4 format
> ccp4
Opened Apo.ccp4 as #1, grid size 440,440,440, pixel 0.65, shown at level 1.94,
step 2, values float32
> open
> /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde_real_space_refined_011.cif
Summary of feedback from opening
/Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde_real_space_refined_011.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 346
Missing entity information. Treating each chain as a separate entity.
Atom H is not in the residue template for ASP /A:8
Atom H is not in the residue template for ASN /D:11
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 29064
Skipping chem_comp category: Missing column 'type' near line 29252
Skipping chem_comp category: Missing column 'type' near line 29395
Skipping chem_comp category: Missing column 'type' near line 29509
Skipping chem_comp category: Missing column 'type' near line 29697
1 messages similar to the above omitted
Chain information for isolde_real_space_refined_011.cif #2
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E | No description available
> isolde start
> set selectionWidth 4
Done loading forcefield
> isolde set simFidelityMode Medium/Medium
ISOLDE: setting sim fidelity mode to Medium/Medium
nonbonded_cutoff_distance = 0.900000
use_gbsa = True
gbsa_cutoff = 1.100000
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 141 residues in model #2 to IUPAC-IUB
standards.
Chain information for isolde_real_space_refined_011.cif
---
Chain | Description
2.2/A | No description available
2.2/B 2.2/C | No description available
2.2/D | No description available
2.2/E | No description available
> clipper associate #1 toModel #2
Opened Apo.ccp4 as #2.1.1.1, grid size 440,440,440, pixel 0.65, shown at step
1, values float32
> volume #2.1.1.1 level 4.676
> select #2.2/D:122
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> delete atoms (#!2.2 & sel)
> delete bonds (#!2.2 & sel)
> ui tool show "Add Hydrogens"
> addh #!2.2
Summary of feedback from adding hydrogens to isolde_real_space_refined_011.cif
#2.2
---
notes | No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2)
chain A; guessing termini instead
No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain B;
guessing termini instead
No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain C;
guessing termini instead
No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain D;
guessing termini instead
No usable SEQRES records for isolde_real_space_refined_011.cif (#2.2) chain E;
guessing termini instead
Chain-initial residues that are actual N termini: /B PRO 6, /C PRO 6, /E PRO 6
Chain-initial residues that are not actual N termini: /A ASP 8, /A ALA 320, /B
GLU 549, /C GLU 549, /D ASN 11, /D ALA 320, /E LYS 552
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini: /A ARG 352, /A PRO 317, /B
SER 584, /B GLN 309, /C SER 584, /C GLN 309, /D ARG 352, /D GLN 316, /E SER
584, /E SER 308
1529 hydrogen bonds
/A ARG 352 is not terminus, removing H atom from 'C'
/B SER 584 is not terminus, removing H atom from 'C'
/C SER 584 is not terminus, removing H atom from 'C'
/D ARG 352 is not terminus, removing H atom from 'C'
/E SER 584 is not terminus, removing H atom from 'C'
3 hydrogens added
> select #2.2/D:276
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> select clear
> volume #2.1.1.1 level 2.033
> select clear
> save /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde.cif
> relModel #2.2
Not saving entity_poly_seq for non-authoritative sequences
> select #2.2/D:276
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> save /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde.cif
> relModel #2.2
Not saving entity_poly_seq for non-authoritative sequences
> select #2.2/D:122
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> ui tool show "Build Structure"
> select clear
> select add #2.2
28440 atoms, 28833 bonds, 60 pseudobonds, 1737 residues, 12 models selected
> isolde sim start /A,D-E,C,B,Z
Loading residue template for BUA from internal database
Loading residue template for EPE from internal database
Sim termination reason: None
ISOLDE: stopped sim
Deleted the following atoms from residue EPE B610: H1, H4
> isolde sim start /B:610
ISOLDE: started sim
> select clear
> select #2.2/D:122
24 atoms, 23 bonds, 1 residue, 1 model selected
> view sel
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: stopped sim
> select #2.2
28438 atoms, 28831 bonds, 60 pseudobonds, 1737 residues, 17 models selected
> isolde sim start /A,D-E,C,B,Z
ISOLDE: started sim
> isolde sim stop
Sim termination reason: None
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 21 residues in model #2.2 to IUPAC-IUB
standards.
ISOLDE: stopped sim
> save /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_11/isolde.cif
> relModel #2.2
Not saving entity_poly_seq for non-authoritative sequences
> close session
> open
> /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/isolde_real_space_refined_012.cif
Summary of feedback from opening
/Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/isolde_real_space_refined_012.cif
---
warnings | Skipping chem_comp category: Missing column 'type' near line 252
Missing entity information. Treating each chain as a separate entity.
Atom H is not in the residue template for ASP /A:8
Atom H is not in the residue template for ASN /D:11
Missing or incomplete sequence information. Inferred polymer connectivity.
Skipping chem_comp category: Missing column 'type' near line 28970
Skipping chem_comp category: Missing column 'type' near line 29158
Skipping chem_comp category: Missing column 'type' near line 29301
Skipping chem_comp category: Missing column 'type' near line 29489
Skipping chem_comp category: Missing column 'type' near line 29603
1 messages similar to the above omitted
Chain information for isolde_real_space_refined_012.cif #1
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E | No description available
ISOLDE: Checking and correcting nomenclature for (pseudo)symmetric side
chains...
ISOLDE: Corrected atom nomenclature of 143 residues in model #1 to IUPAC-IUB
standards.
Chain information for isolde_real_space_refined_012.cif
---
Chain | Description
1.2/A | No description available
1.2/B 1.2/C | No description available
1.2/D | No description available
1.2/E | No description available
> open /Users/johncowgill/Desktop/a5b3/ApoLMNG/Autosharpen_1/Apo.ccp4
Opened Apo.ccp4 as #2, grid size 440,440,440, pixel 0.65, shown at level 1.94,
step 2, values float32
> clipper associate #2 toModel #1
Opened Apo.ccp4 as #1.1.1.1, grid size 440,440,440, pixel 0.65, shown at step
1, values float32
> select #1.2/A:94
11 atoms, 10 bonds, 1 residue, 1 model selected
> view sel
> volume #1.1.1.1 level 2.837
> select #1.2/D:61
15 atoms, 14 bonds, 1 residue, 1 model selected
> view sel
> select #1.2/E:43
12 atoms, 11 bonds, 1 residue, 1 model selected
> view sel
> save
> /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif
> relModel #1.2
Not saving entity_poly_seq for non-authoritative sequences
> close session
> open
> /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif
Summary of feedback from opening
/Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif
---
warnings | Unknown polymer entity '1' near line 226
Unknown polymer entity '2' near line 5834
Unknown polymer entity '3' near line 17437
Unknown polymer entity '4' near line 22943
Atom H is not in the residue template for ASP /A:8
Atom H is not in the residue template for ASN /D:11
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for Resting_Final.cif #1
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E | No description available
> hide atoms
> show cartoons
> measure buriedarea #4/B:1-220 withAtoms2 #4/C:1-220
Buried area between #4/B:1-220 and #4/C:1-220 = 0
area #4/B:1-220 = 0, area #4/C:1-220 = 0, area both = 0
> measure buriedarea #1/B:1-220 withAtoms2 #1/C:1-220
Buried area between #1/B:1-220 and #1/C:1-220 = 1242.7
area #1/B:1-220 = 12270, area #1/C:1-220 = 12442, area both = 22226
> measure buriedarea #1/B:1-220 withAtoms2 #1/A:1-220
Buried area between #1/B:1-220 and #1/A:1-220 = 1351.9
area #1/B:1-220 = 12270, area #1/A:1-220 = 12126, area both = 21692
> measure buriedarea #1/C:1-220 withAtoms2 #1/A:1-220
Buried area between #1/C:1-220 and #1/A:1-220 = 0
area #1/C:1-220 = 12442, area #1/A:1-220 = 12126, area both = 24568
> measure buriedarea #1/E:1-220 withAtoms2 #1/A:1-220
Buried area between #1/E:1-220 and #1/A:1-220 = 1446.1
area #1/E:1-220 = 12371, area #1/A:1-220 = 12126, area both = 21605
> measure buriedarea #1/D:1-220 withAtoms2 #1/E:1-220
Buried area between #1/D:1-220 and #1/E:1-220 = 1421.1
area #1/D:1-220 = 12301, area #1/E:1-220 = 12371, area both = 21830
> measure buriedarea #1/C:1-220 withAtoms2 #1/D:1-220
Buried area between #1/C:1-220 and #1/D:1-220 = 1537.4
area #1/C:1-220 = 12442, area #1/D:1-220 = 12301, area both = 21668
> measure buriedarea #1/B:1-220 withAtoms2 #1/C:1-220
Buried area between #1/B:1-220 and #1/C:1-220 = 1242.7
area #1/B:1-220 = 12270, area #1/C:1-220 = 12442, area both = 22226
> open /Users/johncowgill/Desktop/a5b3/GABAbound.pdb
Summary of feedback from opening /Users/johncowgill/Desktop/a5b3/GABAbound.pdb
---
warning | Ignored bad PDB record found on line 1
Chain information for GABAbound.pdb #2
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E | No description available
P | No description available
> measure buriedarea #2/B:1-220 withAtoms2 #2/C:1-220
Buried area between #2/B:1-220 and #2/C:1-220 = 1425.2
area #2/B:1-220 = 12366, area #2/C:1-220 = 12477, area both = 21993
> measure buriedarea #2/B:1-220 withAtoms2 #2/A:1-220
Buried area between #2/B:1-220 and #2/A:1-220 = 1553.6
area #2/B:1-220 = 12366, area #2/A:1-220 = 12523, area both = 21781
> measure buriedarea #2/B:1-220 withAtoms2 #2/C:1-220
Buried area between #2/B:1-220 and #2/C:1-220 = 1425.2
area #2/B:1-220 = 12366, area #2/C:1-220 = 12477, area both = 21993
> measure buriedarea #2/D:1-220 withAtoms2 #2/C:1-220
Buried area between #2/D:1-220 and #2/C:1-220 = 1539.2
area #2/D:1-220 = 12298, area #2/C:1-220 = 12477, area both = 21697
> measure buriedarea #2/D:1-220 withAtoms2 #2/E:1-220
Buried area between #2/D:1-220 and #2/E:1-220 = 1551.4
area #2/D:1-220 = 12298, area #2/E:1-220 = 12371, area both = 21566
> measure buriedarea #2/D:E:220-588 withAtoms2 #2/E:220-588
Buried area between #2/D:E:220-588 and #2/E:220-588 = 952.67
area #2/D:E:220-588 = 10144, area #2/E:220-588 = 7926.2, area both = 16165
> measure buriedarea #1/D:E:220-588 withAtoms2 #1/E:220-588
Buried area between #1/D:E:220-588 and #1/E:220-588 = 1330.7
area #1/D:E:220-588 = 9759.6, area #1/E:220-588 = 7861.4, area both = 14960
> measure buriedarea #1/D:E withAtoms2 #1/E
Buried area between #1/D:E and #1/E = 0
area #1/D:E = 0, area #1/E = 19864, area both = 19864
> measure buriedarea #1/D withAtoms2 #1/E
Buried area between #1/D and #1/E = 2840.3
area #1/D = 19253, area #1/E = 19864, area both = 33436
> measure buriedarea #1/D:E:220-588 withAtoms2 #1/E:220-588
Buried area between #1/D:E:220-588 and #1/E:220-588 = 1330.7
area #1/D:E:220-588 = 9759.6, area #1/E:220-588 = 7861.4, area both = 14960
> measure buriedarea #1/D:E:1-220 withAtoms2 #1/E:1-220
Buried area between #1/D:E:1-220 and #1/E:1-220 = 1421.1
area #1/D:E:1-220 = 12301, area #1/E:1-220 = 12371, area both = 21830
> measure buriedarea #1/D:E:1-588 withAtoms2 #1/E:1-588
Buried area between #1/D:E:1-588 and #1/E:1-588 = 2830.7
area #1/D:E:1-588 = 19253, area #1/E:1-588 = 18712, area both = 32304
> measure buriedarea #1/D:1-588 withAtoms2 #1/E:1-588
Buried area between #1/D:1-588 and #1/E:1-588 = 2830.7
area #1/D:1-588 = 19253, area #1/E:1-588 = 18712, area both = 32304
> hide atoms
> show cartoons
> hide #!1 models
> select
> ::name="ABU"::name="BMA"::name="BUA"::name="EPE"::name="MAN"::name="NAG"::name="ZN"
1839 atoms, 1884 bonds, 77 residues, 2 models selected
> show (#!2 & sel) target ab
> select up
51665 atoms, 52363 bonds, 3167 residues, 2 models selected
> measure buriedarea #1/D:E:1-588 withAtoms2 #1/E:1-588
Buried area between #1/D:E:1-588 and #1/E:1-588 = 2830.7
area #1/D:E:1-588 = 19253, area #1/E:1-588 = 18712, area both = 32304
> measure buriedarea #1/D:1-588 withAtoms2 #1/E:1-588
Buried area between #1/D:1-588 and #1/E:1-588 = 2830.7
area #1/D:1-588 = 19253, area #1/E:1-588 = 18712, area both = 32304
> measure buriedarea #1/D:1-219 withAtoms2 #1/E:1-219
Buried area between #1/D:1-219 and #1/E:1-219 = 1421.1
area #1/D:1-219 = 12358, area #1/E:1-219 = 12172, area both = 21688
> measure buriedarea #1/D:220-588 withAtoms2 #1/E:220-588
Buried area between #1/D:220-588 and #1/E:220-588 = 1330.7
area #1/D:220-588 = 9759.6, area #1/E:220-588 = 7861.4, area both = 14960
> measure buriedarea #1/B:1-219 withAtoms2 #1/C:1-219
Buried area between #1/B:1-219 and #1/C:1-219 = 1242.7
area #1/B:1-219 = 12074, area #1/C:1-219 = 12294, area both = 21883
> measure buriedarea #1/B:1-219 withAtoms2 #1/C:1-584
Buried area between #1/B:1-219 and #1/C:1-584 = 1372.2
area #1/B:1-219 = 12074, area #1/C:1-584 = 19189, area both = 28519
> measure buriedarea #1/B:1-584 withAtoms2 #1/C:1-584
Buried area between #1/B:1-584 and #1/C:1-584 = 2692.4
area #1/B:1-584 = 18858, area #1/C:1-584 = 19189, area both = 32663
> measure buriedarea #1/B:1-219 withAtoms2 #1/C:1-219
Buried area between #1/B:1-219 and #1/C:1-219 = 1242.7
area #1/B:1-219 = 12074, area #1/C:1-219 = 12294, area both = 21883
> measure buriedarea #1/B:219-585 withAtoms2 #1/C:219-585
Buried area between #1/B:219-585 and #1/C:219-585 = 1351.2
area #1/B:219-585 = 8159, area #1/C:219-585 = 8374.7, area both = 13831
> measure buriedarea #1/B:220-585 withAtoms2 #1/C:220-585
Buried area between #1/B:220-585 and #1/C:220-585 = 1349.1
area #1/B:220-585 = 8131.7, area #1/C:220-585 = 8351.6, area both = 13785
> measure buriedarea #1/B:220-585 withAtoms2 #1/C:1-220
Buried area between #1/B:220-585 and #1/C:1-220 = 0
area #1/B:220-585 = 8131.7, area #1/C:1-220 = 12442, area both = 20573
> measure buriedarea #1/C:220-585 withAtoms2 #1/B:1-220
Buried area between #1/C:220-585 and #1/B:1-220 = 230.99
area #1/C:220-585 = 8351.6, area #1/B:1-220 = 12270, area both = 20159
> close session
> open /Users/johncowgill/Desktop/a5b3/SapGABALong/map/refine201.mrc format
> mrc
Opened refine201.mrc as #1, grid size 440,440,440, pixel 0.648, shown at level
0.000503, step 2, values float32
> volume #1 level 0.0008984
> volume #1 level 0.001109
> close session
> open /Users/johncowgill/Desktop/a5b3/ECDoverlay.cxs
Opened refine201.mrc as #2, grid size 440,440,440, pixel 0.648, shown at level
0.000978, step 2, values float32
opened ChimeraX session
> ui tool show "Side View"
> show (sel-residues & sidechain) target ab
> style sel stick
Changed 48 atom styles
> color sel byhetero
> select H
42627 atoms, 5218 residues, 3 models selected
> delete atoms (#!1,4 & sel)
> delete bonds (#!1,4 & sel)
> select #1/B:ABU
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel target ab
> color sel byhetero
> cofr showPivot false
> view sel
> select clear
> show sel atoms
> style sel stick
Changed 14 atom styles
> color sel byhetero
> select #1/B:ABU
7 atoms, 6 bonds, 1 residue, 1 model selected
> style sel ball
Changed 7 atom styles
> style sel stick
Changed 18 atom styles
> show sel atoms
> color sel byhetero
> view sel
> graphics silhouettes width1
Expected true or false or a keyword
> graphics silhouettes width 1
> select clear
> style sel stick
Changed 24 atom styles
> show sel atoms
> color sel byhetero
> select up
116 atoms, 118 bonds, 14 residues, 2 models selected
> select up
5162 atoms, 5305 bonds, 626 residues, 2 models selected
> select up
5180 atoms, 5321 bonds, 628 residues, 2 models selected
> select down
5162 atoms, 5305 bonds, 626 residues, 2 models selected
> select clear
> select #4/B:BUA
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel stick
Changed 6 atom styles
> show sel atoms
> style sel ball
Changed 6 atom styles
> color sel byhetero
> style sel stick
Changed 22 atom styles
> show sel atoms
> select ~sel & ##selected
28553 atoms, 29340 bonds, 10 pseudobonds, 3479 residues, 5 models selected
> select #1,4
28575 atoms, 29362 bonds, 10 pseudobonds, 3481 residues, 5 models selected
> transparency sel 20
> transparency sel 20 ribbons
> select clear
> ui tool show Distances
> distance #4/B:202@CB #1/B:202@CB
Distance between ApoA5B3-coot-0.pdb #4/B THR 202 CB and
isolde_real_space_refined_018.pdb #1/B THR 202 CB: 1.714Å
> select clear
> hide #!5 models
> hide #5.1 models
> open
> /Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif
Summary of feedback from opening
/Users/johncowgill/Desktop/a5b3/ApoLMNG/RealSpaceRefine_12/Resting_Final.cif
---
warnings | Unknown polymer entity '1' near line 226
Unknown polymer entity '2' near line 5834
Unknown polymer entity '3' near line 17437
Unknown polymer entity '4' near line 22943
Atom H is not in the residue template for ASP /A:8
Atom H is not in the residue template for ASN /D:11
Missing or incomplete sequence information. Inferred polymer connectivity.
Chain information for Resting_Final.cif #6
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E | No description available
> hide #!1,4,6 atoms
> show #!1,4,6 cartoons
> select #6/A:1-222
3401 atoms, 3442 bonds, 215 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #6/A & sel to #4/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker ApoA5B3-coot-0.pdb, chain A (#4) with Resting_Final.cif, chain A
(#6), sequence alignment score = 1112.8
RMSD between 215 pruned atom pairs is 0.097 angstroms; (across all 215 pairs:
0.097)
> select #6/A:1-222
3401 atoms, 3442 bonds, 215 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #6/A & sel to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker isolde_real_space_refined_018.pdb, chain A (#1) with
Resting_Final.cif, chain A (#6), sequence alignment score = 1104.4
RMSD between 211 pruned atom pairs is 0.638 angstroms; (across all 215 pairs:
0.723)
> select #6/A:BUA
Nothing selected
> select #6/B:BUA
13 atoms, 12 bonds, 1 residue, 1 model selected
> show sel target ab
> select H
28375 atoms, 3474 residues, 2 models selected
> delete atoms (#!6 & sel)
> delete bonds (#!6 & sel)
> hide #!4 models
> show sel target ab
> style sel stick
Changed 36 atom styles
> color sel byhetero
> show sel target ab
> style sel stick
Changed 42 atom styles
> color sel byhetero
> select #1/B:ABU
7 atoms, 6 bonds, 1 residue, 1 model selected
> show sel atoms
> select #6/A:BUA
Nothing selected
> style #!1,6 ball
Changed 28536 atom styles
> undo
> select #6/A:BUA
Nothing selected
> select #6/B:BUA
6 atoms, 5 bonds, 1 residue, 1 model selected
> style sel ball
Changed 6 atom styles
> color #1 #929292ff
> color sel byhetero
> select #1
14280 atoms, 14676 bonds, 4 pseudobonds, 1739 residues, 2 models selected
> color (#!1 & sel) byhetero
> select #6/B:1-590
2785 atoms, 2860 bonds, 1 pseudobond, 340 residues, 2 models selected
> color sel #882255
> color (#!6 & sel) byhetero
> select #6/A:1-450
2817 atoms, 2891 bonds, 1 pseudobond, 348 residues, 2 models selected
> color sel #DDCC77
> color (#!6 & sel) byhetero
> select up
14256 atoms, 14649 bonds, 5 pseudobonds, 1737 residues, 2 models selected
> select up
14256 atoms, 14649 bonds, 8 pseudobonds, 1737 residues, 3 models selected
> select #6/B:BUA
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel #DDCC77
> color sel byhetero
> select clear
> show sel target ab
> style sel stick
Changed 22 atom styles
> hide sel atoms
> open
> /Users/johncowgill/Desktop/a5b3/LMNGGABA/RealSpaceRefine_11/isolde_real_space_refined_011.pdb
Chain information for isolde_real_space_refined_011.pdb #7
---
Chain | Description
A | No description available
B C | No description available
D | No description available
E | No description available
P | No description available
> hide sel atoms
> show sel cartoons
> select add #7
30323 atoms, 30721 bonds, 5 pseudobonds, 1861 residues, 4 models selected
> hide sel atoms
> show sel cartoons
> select #6/A:1-222
1725 atoms, 1766 bonds, 215 residues, 1 model selected
> select #7/A:1-222
3401 atoms, 3442 bonds, 215 residues, 1 model selected
> ui tool show Matchmaker
> matchmaker #7/A & sel to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker isolde_real_space_refined_018.pdb, chain A (#1) with
isolde_real_space_refined_011.pdb, chain A (#7), sequence alignment score =
1071.4
RMSD between 214 pruned atom pairs is 0.419 angstroms; (across all 215 pairs:
0.457)
> select #7/B:ABU
15 atoms, 14 bonds, 1 residue, 1 model selected
> show sel target ab
> hide #!7 models
> show #!7 models
> close session
> open /Volumes/KINGSTON/Fig1/Fig1.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: 1.7.1 (2024-01-23)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 ATI-4.12.7
OpenGL renderer: AMD Radeon Pro 570 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: iMac18,3
Processor Name: Quad-Core Intel Core i5
Processor Speed: 3,4 GHz
Number of Processors: 1
Total Number of Cores: 4
L2 Cache (per Core): 256 KB
L3 Cache: 6 MB
Memory: 24 GB
System Firmware Version: 512.0.0.0.0
OS Loader Version: 577~170
SMC Version (system): 2.41f2
Software:
System Software Overview:
System Version: macOS 13.4.1 (22F82)
Kernel Version: Darwin 22.5.0
Time since boot: 9 days, 21 hours, 21 minutes
Graphics/Displays:
Radeon Pro 570:
Chipset Model: Radeon Pro 570
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x67df
Revision ID: 0x00c5
ROM Revision: 113-D000AA-931
VBIOS Version: 113-D0001A1L-025
EFI Driver Version: 01.00.931
Metal Support: Metal 2
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: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-Clipper: 0.22.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ISOLDE: 1.7.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 17 months ago
| 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 , 17 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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