![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15803 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-13.6-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 0x00007ff8505f0700 (most recent call first):
Garbage-collecting
File "/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in
File "/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 161 in __iter__
File "/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 806 in _find_acceptors
File "/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 498 in find_hbonds
File "/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/cmd.py", line 94 in cmd_hbonds
File "/Users/john.bruce/myApps/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 "/Users/john.bruce/myApps/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 "/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/tool.py", line 52 in run_hbonds
File "/Users/john.bruce/myApps/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 "/Users/john.bruce/myApps/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 "/Users/john.bruce/myApps/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.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.surface._surface, chimerax.pdb_lib._load_libs, 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, lxml._elementpath, lxml.etree, lxml.builder, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 60)
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{
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"procRole" : "Foreground",
"version" : 2,
"userID" : 1540847109,
"deployVersion" : 210,
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"coalitionID" : 49878,
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"captureTime" : "2024-08-21 16:34:12.0077 -0400",
"incident" : "FED12675-7618-4710-90FB-347C881AF21F",
"pid" : 61945,
"cpuType" : "X86-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2024-08-21 14:16:35.4279 -0400",
"procStartAbsTime" : 269949768482922,
"procExitAbsTime" : 276173809034883,
"procName" : "ChimeraX",
"procPath" : "\/Users\/USER\/*\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "8FC64BDC-EBF1-C0EB-016B-2508CE779146",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
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"sleepWakeUUID" : "1B815363-34D3-472E-9D38-DC7A6D684F99",
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"vmRegionInfo" : "0xa9 is not in any region. Bytes before following region: 140737486290775\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe08000-7fffffe09000 [ 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":61945},
"vmregioninfo" : "0xa9 is not in any region. Bytes before following region: 140737486290775\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n shared memory 7fffffe08000-7fffffe09000 [ 4K] r-x\/r-x SM=SHM ",
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"faultingThread" : 0,
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}
===== Log before crash start =====
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
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/john.bruce/Desktop/xtal432-p1-250ns dc1.dsv"
Unrecognized file suffix '.dsv'
> open /Users/john.bruce/Desktop/xtal432-p1-250ns-pdb.pdb
Summary of feedback from opening /Users/john.bruce/Desktop/xtal432-p1-250ns-
pdb.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Accelrys Discovery Studio PDB file
Ignored bad PDB record found on line 2
REMARK Created: 2023-02-27T22:57:05Z
Chain information for xtal432-p1-250ns-pdb.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select /A:1-200
3153 atoms, 3187 bonds, 200 residues, 1 model selected
> select /B:201-277
1236 atoms, 1242 bonds, 77 residues, 1 model selected
> select /C:278-344
1048 atoms, 1054 bonds, 4 pseudobonds, 67 residues, 2 models selected
> select clear
> select add #1.2
4 pseudobonds, 1 model selected
> select /A:1-200
3153 atoms, 3187 bonds, 200 residues, 1 model selected
> hide B
> hide C
> hide /C
> hide /B
> select clear
> close session
> open /Users/john.bruce/Desktop/2cyz.pdb format pdb
No such file/path: /Users/john.bruce/Desktop/2cyz.pdb
> open /Users/john.bruce/Desktop/xtal432-p1-250ns-pdb.pdb
Summary of feedback from opening /Users/john.bruce/Desktop/xtal432-p1-250ns-
pdb.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Accelrys Discovery Studio PDB file
Ignored bad PDB record found on line 2
REMARK Created: 2023-02-27T22:57:05Z
Chain information for xtal432-p1-250ns-pdb.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> help help:user
> select /A:1-200
3153 atoms, 3187 bonds, 200 residues, 1 model selected
> select clear
> select LIG 347
Expected an objects specifier or a keyword
> select LIGAND
Expected an objects specifier or a keyword
> select LIG
Expected an objects specifier or a keyword
> select :LIG
44 atoms, 46 bonds, 1 residue, 1 model selected
> hide :C
> hide protein
> show protein
> hide protein
> select /B
1236 atoms, 1242 bonds, 77 residues, 1 model selected
> select /C
1050 atoms, 1054 bonds, 12 pseudobonds, 69 residues, 3 models selected
> hide sel cartoons
> hide solvent
> hide ion
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /C ZN
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ZN
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide ZN1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> hide /C ZN1
Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword
> coulombic protein
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CY1 (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/p8/rh_vqxyd7pl5f74649t7pxxxdxfxh5/T/tmp8hmxonjm/ante.in.mol2 -fi
mol2 -o
/var/folders/p8/rh_vqxyd7pl5f74649t7pxxxdxfxh5/T/tmp8hmxonjm/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(CY1) ``
(CY1) `Welcome to antechamber 20.0: molecular input file processor.`
(CY1) ``
(CY1) `Info: Finished reading file
(/var/folders/p8/rh_vqxyd7pl5f74649t7pxxxdxfxh5/T/tmp8hmxonjm/ante.in.mol2);
atoms read (23), bonds read (22).`
(CY1) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CY1) ``
(CY1) ``
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CY1) `Info: Total number of electrons: 94; net charge: 0`
(CY1) ``
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(CY1) ``
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(CY1) ``
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CY1) ``
Charges for residue CY1 determined
Coulombic values for xtal432-p1-250ns-pdb.pdb_A SES surface #1.3: minimum,
-14.70, mean -0.21, maximum 15.36
Coulombic values for xtal432-p1-250ns-pdb.pdb_B SES surface #1.4: minimum,
-12.68, mean 0.42, maximum 16.32
Coulombic values for xtal432-p1-250ns-pdb.pdb_C SES surface #1.5: minimum,
-11.28, mean 1.59, maximum 14.21
> coulombic protein key true
Coulombic values for xtal432-p1-250ns-pdb.pdb_A SES surface #1.3: minimum,
-14.70, mean -0.21, maximum 15.36
Coulombic values for xtal432-p1-250ns-pdb.pdb_B SES surface #1.4: minimum,
-12.68, mean 0.42, maximum 16.32
Coulombic values for xtal432-p1-250ns-pdb.pdb_C SES surface #1.5: minimum,
-11.28, mean 1.59, maximum 14.21
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> ui mousemode right translate
> 2dlabels text "electrostatic potential"
> ui mousemode right "move label"
> 2dlabels #3.1 xpos 0.704 ypos 0.621
> 2dlabels #3.1 xpos 0.774 ypos 0.946
> ui mousemode right "color key"
> ui mousemode right "move label"
> select subtract #1.5
49 atoms, 44 bonds, 4 pseudobonds, 6 residues, 3 models selected
> select add #1.5
1050 atoms, 44 bonds, 4 pseudobonds, 69 residues, 2 models selected
> select subtract #1.5
49 atoms, 44 bonds, 4 pseudobonds, 6 residues, 3 models selected
> select add #1.4
1285 atoms, 44 bonds, 4 pseudobonds, 83 residues, 2 models selected
> select subtract #1.4
49 atoms, 44 bonds, 4 pseudobonds, 6 residues, 3 models selected
> select add #1.4
1285 atoms, 44 bonds, 4 pseudobonds, 83 residues, 2 models selected
> select subtract #1.4
49 atoms, 44 bonds, 4 pseudobonds, 6 residues, 3 models selected
> select add #1.3
3202 atoms, 44 bonds, 4 pseudobonds, 206 residues, 2 models selected
> select subtract #1.3
49 atoms, 44 bonds, 4 pseudobonds, 6 residues, 3 models selected
> select add #1.3
3202 atoms, 44 bonds, 4 pseudobonds, 206 residues, 2 models selected
> select subtract #1.3
49 atoms, 44 bonds, 4 pseudobonds, 6 residues, 3 models selected
> select add #1.5
1050 atoms, 44 bonds, 4 pseudobonds, 69 residues, 2 models selected
> select subtract #1.5
49 atoms, 44 bonds, 4 pseudobonds, 6 residues, 3 models selected
> hide /C
> select add #1.5
1050 atoms, 44 bonds, 4 pseudobonds, 69 residues, 2 models selected
> select subtract #1.5
49 atoms, 44 bonds, 4 pseudobonds, 6 residues, 3 models selected
> close session
> open /Users/john.bruce/Desktop/xtal432-p1-250ns-pdb.pdb
Summary of feedback from opening /Users/john.bruce/Desktop/xtal432-p1-250ns-
pdb.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Accelrys Discovery Studio PDB file
Ignored bad PDB record found on line 2
REMARK Created: 2023-02-27T22:57:05Z
Chain information for xtal432-p1-250ns-pdb.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> hide #1.1 models
> show #1.1 models
> hide #1.2 models
> show #1.2 models
> select add #1.2
4 pseudobonds, 1 model selected
> select subtract #1.2
Nothing selected
> select add #1.2
4 pseudobonds, 1 model selected
> select subtract #1.2
Nothing selected
> select add #1.1
8 pseudobonds, 1 model selected
> hide #1.1 models
> select subtract #1.1
Nothing selected
> select add #1
5513 atoms, 5549 bonds, 12 pseudobonds, 357 residues, 3 models selected
> select subtract #1
Nothing selected
> select /A:1-200
3153 atoms, 3187 bonds, 200 residues, 1 model selected
> select /A:1-200
3153 atoms, 3187 bonds, 200 residues, 1 model selected
> select /B:201-277
1236 atoms, 1242 bonds, 77 residues, 1 model selected
> select /B:201-277
1236 atoms, 1242 bonds, 77 residues, 1 model selected
> select /C:278-344
1048 atoms, 1054 bonds, 4 pseudobonds, 67 residues, 2 models selected
> select /C:278-344
1048 atoms, 1054 bonds, 4 pseudobonds, 67 residues, 2 models selected
> hide sel cartoons
> hide sel atoms
> show #1.1 models
> hide #1.1 models
> select ::name="ZN1"
1 atom, 1 residue, 1 model selected
> hide sel cartoons
> hide sel atoms
> select ::name="ZN2"
1 atom, 1 residue, 1 model selected
> hide sel atoms
> mlp
Map values for surface "xtal432-p1-250ns-pdb.pdb_A SES surface": minimum
-24.64, mean -3.092, maximum 23.18
Map values for surface "xtal432-p1-250ns-pdb.pdb_B SES surface": minimum
-25.04, mean -4.881, maximum 21.82
Map values for surface "xtal432-p1-250ns-pdb.pdb_C SES surface": minimum
-23.48, mean 2.415e+05, maximum 1.377e+07
> hide solvent
> surface zone #1 nearAtoms :LIG distance 8 maxComponents 1
> hide ~:LIG target ar
> hide #1.5 models
> show #1.5 models
> hide #1.4 models
> show #1.4 models
> hide #1.3 models
> show #1.3 models
> select clear
> hide #1.4 models
> style stick
Changed 5513 atom styles
> style stick
Changed 5513 atom styles
> style ball
Changed 5513 atom styles
> style ball
Changed 5513 atom styles
> style ball
Changed 5513 atom styles
> style sphere
Changed 5513 atom styles
> style sphere
Changed 5513 atom styles
> style ball
Changed 5513 atom styles
> style stick
Changed 5513 atom styles
> show atoms
> hide atoms
> show :LIG
> clip
> show #1.4 models
> hide #1.4 models
> show #1.4 models
> hide #1.4 models
> select add #1.5
1001 atoms, 63 residues, 1 model selected
> select subtract #1.5
1 model selected
> select add #1.4
1236 atoms, 77 residues, 1 model selected
> select subtract #1.4
1 model selected
> clip model #! off
Missing or invalid "models" argument: invalid models specifier
> hide ~:LIG
> ui tool show "Side View"
> ui mousemode right clip
> ui mousemode right "clip rotate"
> ui mousemode right zone
> mlp protein surfaces #1.1.1
Map values for surface "xtal432-p1-250ns-pdb.pdb_A SES surface": minimum
-24.64, mean -3.092, maximum 23.18
Map values for surface "xtal432-p1-250ns-pdb.pdb_B SES surface": minimum
-25.04, mean -4.881, maximum 21.82
Map values for surface "xtal432-p1-250ns-pdb.pdb_C SES surface": minimum
-23.48, mean 1.598e+05, maximum 8.728e+06
> hide #1.4 models
> transparency #1.1.1 30
> coulombic protein
Using Amber 20 recommended default charges and atom types for standard
residues
Assigning partial charges to residue CY1 (net charge +0) with am1-bcc method
Running ANTECHAMBER command:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber
-ek qm_theory='AM1', -i
/var/folders/p8/rh_vqxyd7pl5f74649t7pxxxdxfxh5/T/tmpunvlfqj6/ante.in.mol2 -fi
mol2 -o
/var/folders/p8/rh_vqxyd7pl5f74649t7pxxxdxfxh5/T/tmpunvlfqj6/ante.out.mol2 -fo
mol2 -c bcc -nc 0 -j 5 -s 2 -dr n
(CY1) ``
(CY1) `Welcome to antechamber 20.0: molecular input file processor.`
(CY1) ``
(CY1) `Info: Finished reading file
(/var/folders/p8/rh_vqxyd7pl5f74649t7pxxxdxfxh5/T/tmpunvlfqj6/ante.in.mol2);
atoms read (23), bonds read (22).`
(CY1) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype
-j part -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`
(CY1) ``
(CY1) ``
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype
-i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`
(CY1) `Info: Total number of electrons: 94; net charge: 0`
(CY1) ``
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm -O -i
sqm.in -o sqm.out`
(CY1) ``
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`
(CY1) ``
(CY1) `Running:
/Users/john.bruce/myApps/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype
-f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`
(CY1) ``
Charges for residue CY1 determined
Coulombic values for xtal432-p1-250ns-pdb.pdb_A SES surface #1.3: minimum,
-14.70, mean -0.21, maximum 15.36
Coulombic values for xtal432-p1-250ns-pdb.pdb_B SES surface #1.4: minimum,
-12.68, mean 0.42, maximum 16.32
Coulombic values for xtal432-p1-250ns-pdb.pdb_C SES surface #1.5: minimum,
-11.28, mean 1.59, maximum 14.21
> coulombic protein
Coulombic values for xtal432-p1-250ns-pdb.pdb_A SES surface #1.3: minimum,
-14.70, mean -0.21, maximum 15.36
Coulombic values for xtal432-p1-250ns-pdb.pdb_B SES surface #1.4: minimum,
-12.68, mean 0.42, maximum 16.32
Coulombic values for xtal432-p1-250ns-pdb.pdb_C SES surface #1.5: minimum,
-11.28, mean 1.59, maximum 14.21
> hide #1.4 models
> hbonds :LIG reveal true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 xtal432-p1-250ns-pdb.pdb
3 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
/? LIG 347 N1 /? WAT 348 O /? LIG 347 HN1 3.089 2.153
/? WAT 354 O /? LIG 347 O3 /? WAT 354 H1 3.026 2.093
/A GLN 26 NE2 /? LIG 347 O4 /A GLN 26 1HE2 3.132 2.249
3 hydrogen bonds found
> close session
> open /Users/john.bruce/Desktop/xtal432-p1-250ns-pdb.pdb
Summary of feedback from opening /Users/john.bruce/Desktop/xtal432-p1-250ns-
pdb.pdb
---
warnings | Ignored bad PDB record found on line 1
REMARK Accelrys Discovery Studio PDB file
Ignored bad PDB record found on line 2
REMARK Created: 2023-02-27T22:57:05Z
Chain information for xtal432-p1-250ns-pdb.pdb #1
---
Chain | Description
A | No description available
B | No description available
C | No description available
> select /A:1-200
3153 atoms, 3187 bonds, 200 residues, 1 model selected
> select /B:201-277
1236 atoms, 1242 bonds, 77 residues, 1 model selected
> select /C:278-344
1048 atoms, 1054 bonds, 4 pseudobonds, 67 residues, 2 models selected
> hide /C
> select clear
> select /A:1-200
3153 atoms, 3187 bonds, 200 residues, 1 model selected
> select /A:1-200
3153 atoms, 3187 bonds, 200 residues, 1 model selected
> select add #1
5513 atoms, 5549 bonds, 12 pseudobonds, 357 residues, 3 models selected
> select subtract #1
Nothing selected
> select add #1.2
4 pseudobonds, 1 model selected
> select subtract #1.2
Nothing selected
> select add #1.1
8 pseudobonds, 1 model selected
> view sel
No displayed objects specified.
> select /C
1050 atoms, 1054 bonds, 12 pseudobonds, 69 residues, 3 models selected
> hide sel cartoons
> ui tool show H-Bonds
> select :LIG
44 atoms, 46 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel reveal true log true
===== Log before crash end =====
Log:
Startup Messages
---
warnings | Replacing fetcher for 'ngff' and format OME-Zarr from OME-Zarr
bundle with that from OME-Zarr bundle
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-4.14.1
OpenGL renderer: AMD Radeon Pro 5300M 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: MacBook Pro
Model Identifier: MacBookPro16,1
Processor Name: 6-Core Intel Core i7
Processor Speed: 2.6 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: 2020.0.1.0.0 (iBridge: 21.16.365.0.0,0)
OS Loader Version: 577.140.2~15
Software:
System Software Overview:
System Version: macOS 13.6 (22G120)
Kernel Version: Darwin 22.6.0
Time since boot: 12 days, 3 hours, 37 minutes
Graphics/Displays:
Intel UHD Graphics 630:
Chipset Model: Intel UHD Graphics 630
Type: GPU
Bus: Built-In
VRAM (Dynamic, Max): 1536 MB
Vendor: Intel
Device ID: 0x3e9b
Revision ID: 0x0000
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
AMD Radeon Pro 5300M:
Chipset Model: AMD Radeon Pro 5300M
Type: GPU
Bus: PCIe
PCIe Lane Width: x16
VRAM (Total): 4 GB
Vendor: AMD (0x1002)
Device ID: 0x7340
Revision ID: 0x0043
ROM Revision: 113-D3220E-190
VBIOS Version: 113-D32207P1-020
Option ROM Version: 113-D32207P1-020
EFI Driver Version: 01.A1.190
Automatic Graphics Switching: Supported
gMux Version: 5.0.0
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-In Retina LCD
Resolution: 3072 x 1920 Retina
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Main Display: Yes
Mirror: Off
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
G276HL:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: LW9AA0048524
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: 0.00
G277HL:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Framebuffer Depth: 30-Bit Color (ARGB2101010)
Display Serial Number: T2NAA0018523
Mirror: Off
Online: Yes
Rotation: Supported
Connection Type: DVI or HDMI
Adapter Firmware Version: b.1d
Installed Packages:
alabaster: 0.7.16
appdirs: 1.4.4
appnope: 0.1.3
asttokens: 2.4.1
Babel: 2.14.0
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
blosc2: 2.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.3
charset-normalizer: 3.3.2
ChimeraX-AddCharge: 1.5.13
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.4.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.12.2
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.1.1
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.49.1
ChimeraX-AtomicLibrary: 12.1.5
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.10.5
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.3.2
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.5
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.7.1
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-Label: 1.1.8
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.1.6
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.2
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.6.1
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12.1
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.14
ChimeraX-ModelPanel: 1.4
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.1
ChimeraX-NRRD: 1.1
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.13.1
ChimeraX-PDB: 2.7.3
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.2
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.11
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.2
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.12.4
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.33.3
ChimeraX-uniprot: 2.3
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.3.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.3
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.1
contourpy: 1.2.0
cxservices: 1.2.2
cycler: 0.12.1
Cython: 0.29.33
debugpy: 1.8.0
decorator: 5.1.1
docutils: 0.19
executing: 2.0.1
filelock: 3.9.0
fonttools: 4.47.2
funcparserlib: 2.0.0a0
glfw: 2.6.4
grako: 3.16.5
h5py: 3.10.0
html2text: 2020.1.16
idna: 3.6
ihm: 0.38
imagecodecs: 2023.9.18
imagesize: 1.4.1
ipykernel: 6.23.2
ipython: 8.14.0
ipython-genutils: 0.2.0
ipywidgets: 8.1.1
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.2.0
jupyter-core: 5.7.1
jupyterlab-widgets: 3.0.9
kiwisolver: 1.4.5
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.4
matplotlib: 3.7.2
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.6.0
netCDF4: 1.6.2
networkx: 3.1
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.8
numpy: 1.25.1
openvr: 1.23.701
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 10.2.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 4.1.0
prompt-toolkit: 3.0.43
psutil: 5.9.5
ptyprocess: 0.7.0
pure-eval: 0.2.2
py-cpuinfo: 9.0.0
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.16.1
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.2801
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.3.1
PyQt6-Qt6: 6.3.2
PyQt6-sip: 13.4.0
PyQt6-WebEngine-commercial: 6.3.1
PyQt6-WebEngine-Qt6: 6.3.2
python-dateutil: 2.8.2
pytz: 2023.3.post1
pyzmq: 25.1.2
qtconsole: 5.4.3
QtPy: 2.4.1
RandomWords: 0.4.0
requests: 2.31.0
scipy: 1.11.1
setuptools: 67.4.0
setuptools-scm: 7.0.5
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.5
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.8
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.6
sphinxcontrib-htmlhelp: 2.0.5
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.7
sphinxcontrib-serializinghtml: 1.1.10
stack-data: 0.6.3
superqt: 0.5.0
tables: 3.8.0
tcia-utils: 1.5.1
tifffile: 2023.7.18
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.4
traitlets: 5.9.0
typing-extensions: 4.9.0
tzdata: 2023.4
urllib3: 2.1.0
wcwidth: 0.2.13
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.9
Change History (2)
comment:1 by , 14 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 , 14 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | accepted → closed |
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