Opened 17 months ago

Closed 17 months ago

#15254 closed defect (duplicate)

Crash in garbage collection

Reported by: carlton.petermark.3v@… 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 (last modified by Eric Pettersen) 

The following bug report has been submitted:
Platform:        macOS-12.7.1-x86_64-i386-64bit
ChimeraX Version: 1.9.dev202405110020 (2024-05-11 00:20:53 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x0000700004a6e000 (most recent call first):
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 324 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 622 in wait
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1392 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00000001103c0600 (most recent call first):
  Garbage-collecting
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/ctypes/__init__.py", line 512 in cast
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/core/_internal.py", line 282 in data_as
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 333 in pointer
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/molc.py", line 223 in set_prop
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/color.py", line 273 in _set_atom_colors
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/color.py", line 536 in _set_sequential_residue
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/color.py", line 1068 in color_sequential
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/std_commands/rainbow.py", line 19 in rainbow
  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/shortcuts/shortcuts.py", line 525 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 582 in run_expanded_command
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 339 in run
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 420 in run_shortcut
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 402 in try_shortcut
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/shortcuts.py", line 1376 in run_provider
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/shortcuts/__init__.py", line 66 in run_provider
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/__init__.py", line 1302 in run_provider
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/toolshed/info.py", line 397 in run_provider
  File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/toolbar/tool.py", line 205 in callback
  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, lxml._elementpath, lxml.etree, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 59)


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  "parentPid" : 1,
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  "crashReporterKey" : "B9141A2B-BB6A-AD8E-3FB5-46A0DD310398",
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  "vmRegionInfo" : "0xa9 is not in any region.  Bytes before following region: 140737486774103\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      VM_ALLOCATE              7fffffe7e000-7fffffe7f000 [    4K] r-x\/r-x SM=ALI  ",
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  "vmregioninfo" : "0xa9 is not in any region.  Bytes before following region: 140737486774103\n      REGION TYPE                    START - END         [ VSIZE] PRT\/MAX SHRMOD  REGION DETAIL\n      UNUSED SPACE AT START\n--->  \n      VM_ALLOCATE              7fffffe7e000-7fffffe7f000 [    4K] r-x\/r-x SM=ALI  ",
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  "usedImages" : [
[deleted to fit within ticket limits]
}
===== 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/pcarlton/Desktop/quickref/DSB_1_2_3relaxed.pdb

Chain information for DSB_1_2_3relaxed.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
  

> color bychain

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

> select /C:40

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /C:40-43

56 atoms, 57 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 56 atom styles  

> select /C:77

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /C:77-80

70 atoms, 71 bonds, 4 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 70 atom styles  

> select clear

> style sphere

Changed 16040 atom styles  

> select /B:164

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /B:164-166

51 atoms, 52 bonds, 3 residues, 1 model selected  

> select /B:266

20 atoms, 20 bonds, 1 residue, 1 model selected  

> select /B:266-269

68 atoms, 70 bonds, 4 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 17 residues  
Drag select of 2 residues  

> select up

417 atoms, 425 bonds, 26 residues, 1 model selected  

> select clear

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23/fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_0.cif

Chain information for
fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_0.cif #2  
---  
Chain | Description  
A | .  
B | .  
  

> close #1

> color bychain

> select clear

> color bypolymer

> select protein

4838 atoms, 4963 bonds, 598 residues, 1 model selected  

> select clear

> color dim gray

> select clear

> select protein

4838 atoms, 4963 bonds, 598 residues, 1 model selected  

> color sel bypolymer

> color sel bychain

> select clear

> select /A:26

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

123 atoms, 122 bonds, 16 residues, 1 model selected  

> select up

1023 atoms, 1049 bonds, 125 residues, 1 model selected  

> select clear

Alignment identifier is 2/A  
Alignment identifier is 2/B  

> ui tool show Contacts

> contacts resSeparation 8 interModel false intraMol false ignoreHiddenModels
> true select true color #c349c3 dashes 0 radius 0.05 reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Ignore contacts between atoms in residues less than 8 apart in sequence
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    514 contacts
        atom1           atom2       overlap  distance
    /B MET 428 CE   /A LEU 16 CD2    1.183    2.577
[deleted to fit within ticket limits]
    /A PHE 83 CZ    /L OLA 1 C8      -0.399    3.919
    

  
514 contacts  

> select clear

> hide atoms

> close #2.1

> select clear

Drag select of 18 residues  

> select up

709 atoms, 723 bonds, 86 residues, 1 model selected  

> select up

4838 atoms, 4963 bonds, 598 residues, 1 model selected  

> contacts sel restrict both resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Ignore contacts between atoms in residues less than 8 apart in sequence
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    204 contacts
        atom1           atom2       overlap  distance
    /A LEU 16 CD2   /B MET 428 CE    1.183    2.577
[deleted to fit within ticket limits]
    /B PRO 37 CA    /A ASN 35 O      -0.399    3.699
    

  
204 contacts  

> close

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23/fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_1.cif

Chain information for
fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_1.cif #1  
---  
Chain | Description  
A | .  
B | .  
  

> select protein

4838 atoms, 4963 bonds, 598 residues, 1 model selected  
Alignment identifier is 1/A  
Alignment identifier is 1/B  

> contacts sel restrict both resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Ignore contacts between atoms in residues less than 8 apart in sequence
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    143 contacts
        atom1           atom2       overlap  distance
    /A LYS 21 CD    /B GLU 398 OE2   1.115    2.185
[deleted to fit within ticket limits]
    /B ARG 266 CG   /A ARG 22 CZ     -0.397    3.887
    

  
143 contacts  

> color sel red

> color sel bychain

> select clear

> select /A:20

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select up

338 atoms, 344 bonds, 43 residues, 1 model selected  

> color sel byhetero

> select up

1023 atoms, 1049 bonds, 125 residues, 1 model selected  

> select down

338 atoms, 344 bonds, 43 residues, 1 model selected  

> show sel atoms

> color sel byhetero

> style sel ball

Changed 338 atom styles  

> color sel bychain

> select clear

> select /B:420

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select add /B:368

19 atoms, 17 bonds, 2 residues, 1 model selected  

> select /B:103

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select /B:103-131

252 atoms, 259 bonds, 29 residues, 1 model selected  

> color sel cyan

> select /A:92

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select up

152 atoms, 155 bonds, 19 residues, 1 model selected  

> select add /A:118

164 atoms, 167 bonds, 20 residues, 1 model selected  

> select up

294 atoms, 301 bonds, 36 residues, 1 model selected  

> select /A:75

9 atoms, 8 bonds, 1 residue, 1 model selected  

> select /A:75-103

239 atoms, 247 bonds, 29 residues, 1 model selected  

> color sel cyan

> select /A:119

11 atoms, 11 bonds, 1 residue, 1 model selected  

> select up

142 atoms, 146 bonds, 17 residues, 1 model selected  

> select /B:8

10 atoms, 9 bonds, 1 residue, 1 model selected  

> select /B:8

10 atoms, 9 bonds, 1 residue, 1 model selected  

> contacts sel resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Ignore contacts between atoms in residues less than 8 apart in sequence
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    3 contacts
       atom1         atom2      overlap  distance
    /B SEP 8 CB   /A PRO 41 CB   -0.176    3.816
    /B SEP 8 N    /A PRO 41 CB   -0.201    3.721
    /B SEP 8 O2P  /A PRO 41 CB   -0.261    3.561
    

  
3 contacts  

> select clear

> select /B:99

11 atoms, 10 bonds, 1 residue, 1 model selected  

> select up

260 atoms, 267 bonds, 27 residues, 1 model selected  

> select up

3815 atoms, 3914 bonds, 473 residues, 1 model selected  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue SEP (net charge -2) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpqmbj5jk3/ante.in.mol2 -fi
mol2 -o
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpqmbj5jk3/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(SEP) ``  
(SEP) `Welcome to antechamber 20.0: molecular input file processor.`  
(SEP) ``  
(SEP) `Info: Finished reading file
(/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpqmbj5jk3/ante.in.mol2);
atoms read (27), bonds read (26).`  
(SEP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(SEP) ``  
(SEP) ``  
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(SEP) `Info: Total number of electrons: 132; net charge: -2`  
(SEP) ``  
(SEP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`  
(SEP) ``  
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(SEP) ``  
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(SEP) ``  
Charges for residue SEP determined  
Coulombic values for
fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_1.cif_B SES surface #1.2:
minimum, -20.78, mean -1.07, maximum 12.52  
To also show corresponding color key, enter the above coulombic command and
add key true  

> mlp sel

Map values for surface
"fold_mjl_1_50xoleic_sun_1_s8p_2024_05_20_12_23_model_1.cif_B SES surface":
minimum -28.02, mean 4.821e+12, maximum 1.704e+15  
To also show corresponding color key, enter the above mlp command and add key
true  

> undo

> select clear

> select /A:14

6 atoms, 5 bonds, 1 residue, 1 model selected  

> select up

338 atoms, 344 bonds, 43 residues, 1 model selected  

> contacts sel resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Ignore contacts between atoms in residues less than 8 apart in sequence
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    126 contacts
        atom1          atom2       overlap  distance
    /A LYS 21 CD   /B GLU 398 OE2   1.115    2.185
[deleted to fit within ticket limits]
    /A ARG 22 CZ   /B ARG 266 CG    -0.397    3.887
    

  
126 contacts  

> select clear

> hide surfaces

> select clear

Drag select of 5 atoms, 6 bonds  

> select up

8 atoms, 6 bonds, 2 residues, 1 model selected  

> select up

40 atoms, 38 bonds, 2 residues, 1 model selected  

> select up

5838 atoms, 5913 bonds, 648 residues, 1 model selected  

> select down

40 atoms, 38 bonds, 2 residues, 2 models selected  

> select clear

> select protein

4838 atoms, 4963 bonds, 126 pseudobonds, 598 residues, 2 models selected  

> select ~sel & ##selected

1000 atoms, 950 bonds, 50 residues, 1 model selected  

> hide sel atoms

> select clear

> color bychain

Drag select of 2 residues  

> select up

445 atoms, 454 bonds, 54 residues, 2 models selected  

> select up

3815 atoms, 3914 bonds, 473 residues, 2 models selected  

> select clear

> close

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_0.cif

Summary of feedback from opening
/Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_0.cif  
---  
notes | Fetching CCD PLM from https://files.wwpdb.org/pub/pdb/refdata/chem_comp/M/PLM/PLM.cif  
Fetching CCD MYR from
https://files.wwpdb.org/pub/pdb/refdata/chem_comp/R/MYR/MYR.cif  
  
Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_0.cif
#1  
---  
Chain | Description  
A | .  
B C D | .  
  

> color dark gray

> select protein

12468 atoms, 12791 bonds, 1544 residues, 1 model selected  

> color sel bychain

> color sel bypolymer

Alignment identifier is 1/A  
Alignment identifier is 1  

> select clear

> select /A:125

12 atoms, 12 bonds, 1 residue, 1 model selected  

> select /A

1023 atoms, 1049 bonds, 125 residues, 1 model selected  

> color sel orange

> select clear

Drag select of 34 residues  

> select clear

Drag select of 55 residues  

> select
> /B,C,D:8-15,18-27,36-43,45-67,69-76,79-105,109-134,144-237,244-251,254-269,276-278,284-286,297-305,310-314,375-377,450-472

6771 atoms, 6888 bonds, 822 residues, 1 model selected  

> select clear

> select /B,C,D:101

21 atoms, 18 bonds, 3 residues, 1 model selected  

> select /B,C,D:101-143

1083 atoms, 1113 bonds, 129 residues, 1 model selected  

> select clear

> select /B,C,D:103

33 atoms, 30 bonds, 3 residues, 1 model selected  

> select /B,C,D:103-131

756 atoms, 777 bonds, 87 residues, 1 model selected  

> close

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif

Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif
#1  
---  
Chain | Description  
A | .  
B C D | .  
  

> select protein

12468 atoms, 12791 bonds, 1544 residues, 1 model selected  

> color sel bychain

> color sel bypolymer

> select clear

Drag select of 13 residues  

> select up

175 atoms, 178 bonds, 23 residues, 1 model selected  

> select up

1023 atoms, 1049 bonds, 125 residues, 1 model selected  

> contacts sel resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Ignore contacts between atoms in residues less than 8 apart in sequence
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    401 contacts
        atom1           atom2       overlap  distance
    /A ASN 35 CB    /C VAL 319 CG2   1.520    2.240
[deleted to fit within ticket limits]
    /A PRO 41 CG    /D ARG 4 CZ      -0.397    3.887
    

  
401 contacts  
Alignment identifier is 1/A  
Alignment identifier is 1  

> coulombic sel

Using Amber 20 recommended default charges and atom types for standard
residues  
Assigning partial charges to residue SEP (net charge -2) with am1-bcc method  
Running ANTECHAMBER command:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/antechamber -ek
qm_theory='AM1', -i
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpjah3s45g/ante.in.mol2 -fi
mol2 -o
/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpjah3s45g/ante.out.mol2 -fo
mol2 -c bcc -nc -2 -j 5 -s 2 -dr n  
(SEP) ``  
(SEP) `Welcome to antechamber 20.0: molecular input file processor.`  
(SEP) ``  
(SEP) `Info: Finished reading file
(/var/folders/yt/5k_s5pc12px36mv2_95d4qq40000gn/T/tmpjah3s45g/ante.in.mol2);
atoms read (29), bonds read (28).`  
(SEP) `Info: Determining atomic numbers from atomic symbols which are case
sensitive.`  
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/bondtype -j part -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac`  
(SEP) ``  
(SEP) ``  
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -i
ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff`  
(SEP) `Info: Total number of electrons: 134; net charge: -2`  
(SEP) ``  
(SEP) `Running: /Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/sqm
-O -i sqm.in -o sqm.out`  
(SEP) ``  
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/am1bcc -i
ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/dat/antechamber/BCCPARM.DAT
-s 2 -j 1`  
(SEP) ``  
(SEP) `Running:
/Applications/ChimeraX-1.7.1.app/Contents/bin/amber20/bin/atomtype -f ac -p
bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC`  
(SEP) ``  
Charges for residue SEP determined  
Coulombic values for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif_A
SES surface #1.2: minimum, -16.29, mean -1.79, maximum 11.14  
Coulombic values for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif_B
SES surface #1.3: minimum, -18.79, mean -1.13, maximum 11.88  
Coulombic values for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif_C
SES surface #1.4: minimum, -19.34, mean -1.13, maximum 11.59  
Coulombic values for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_1.cif_D
SES surface #1.5: minimum, -19.99, mean -1.27, maximum 12.70  
To also show corresponding color key, enter the above coulombic command and
add key true  
Drag select of 9 residues  

> select up

1243 atoms, 1264 bonds, 170 residues, 4 models selected  

> select clear

> select /A:33

7 atoms, 7 bonds, 1 residue, 1 model selected  

> select /A:33-42

83 atoms, 86 bonds, 10 residues, 1 model selected  

> select clear

> hide surfaces

> select /B,C,D:103

33 atoms, 30 bonds, 3 residues, 1 model selected  

> select /B,C,D:103-131

756 atoms, 777 bonds, 87 residues, 1 model selected  

> close

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_2.cif

Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_2.cif
#1  
---  
Chain | Description  
A | .  
B C D | .  
  

> select /C:260

7 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> show sel cartoons

> show sel atoms

> style sel sphere

Changed 7 atom styles  

> close

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_3.cif

Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_3.cif
#1  
---  
Chain | Description  
A | .  
B C D | .  
  
Drag select of 7 residues  
Alignment identifier is 1  

> select clear

Drag select of 2 residues  

> select clear

> select /D:227

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel cartoons

> select clear

> select /D:227@CG1

1 atom, 1 residue, 1 model selected  

> select add /D:227@CA

1 atom, 1 bond, 1 residue, 1 model selected  

> select add /D:227@C

2 atoms, 1 bond, 1 residue, 1 model selected  

> ui mousemode right "bond rotation"

> torsion /D:227@C /D:227@CA /D:227@N /D:226@C -103.11

> torsion /D:227@CD1,CG1,CB,CA -173.00

> torsion /D:227@CG1,CB,CA,N -64.22

> torsion /D:228@N /D:227@C /D:227@CA /D:227@N -30.05

> torsion /D:228@N /D:227@C /D:227@CA /D:227@N -22.69

> torsion /D:228@N /D:227@C /D:227@CA /D:227@N 45.49

> select clear

> select /B:225

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right "rotate selected models"

> view matrix models
> #1,0.99952,0.019386,0.024107,2.0948,-0.020453,0.99879,0.044825,0.59157,-0.023209,-0.045297,0.9987,-4.0796

> ui mousemode right "bond rotation"

> show sel atoms

> style sel ball

Changed 9 atom styles  

> hide sel cartoons

> torsion /B:226@N /B:225@C /B:225@CA /B:225@N -152.18

> torsion /B:226@N /B:225@C /B:225@CA /B:225@N -127.15

> select /C:227

8 atoms, 7 bonds, 1 residue, 1 model selected  

> show sel atoms

> hide sel cartoons

> torsion /C:227@CG1,CB,CA,N -1.03

> torsion /C:227@CG1,CB,CA,N -20.17

> hide sel cartoons

> torsion /C:227@CG1,CB,CA,N -4.48

> torsion /C:227@C /C:227@CA /C:227@N /C:226@C -78.98

> torsion /C:227@C /C:227@CA /C:227@N /C:226@C -165.65

> select /B,C,D:103

33 atoms, 30 bonds, 3 residues, 1 model selected  

> select /B,C,D:103-159

1428 atoms, 1470 bonds, 171 residues, 1 model selected  

> close

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_3.cif

Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_3.cif
#1  
---  
Chain | Description  
A | .  
B C D | .  
  
Alignment identifier is 1/A  
Alignment identifier is 1  

> select /B,C,D:103

33 atoms, 30 bonds, 3 residues, 1 model selected  

> select /B,C,D:103-131

756 atoms, 777 bonds, 87 residues, 1 model selected  
Drag select of 72 residues  

> show sel atoms

> hide sel cartoons

> select clear

> color bychain

> color bypolymer

> select clear

> color bychain

> select clear

Drag select of 275 atoms, 276 bonds  

> cofr sel

> select clear

Drag select of 18 atoms, 16 bonds  

> select clear

> style ball

Changed 15168 atom styles  

> color byhetero

> select clear

> select /C:227@O

1 atom, 1 residue, 1 model selected  

> select /C:227@C

1 atom, 1 residue, 1 model selected  

> select /C:227@CA

1 atom, 1 residue, 1 model selected  

> close

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_4.cif

Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_4.cif
#1  
---  
Chain | Description  
A | .  
B C D | .  
  

> select /A:1-125

1023 atoms, 1049 bonds, 125 residues, 1 model selected  

> show sel atoms

> style sel sphere

Changed 1023 atom styles  

> color sel byhetero

> select clear

Drag select of 27 residues  

> select up

3377 atoms, 3442 bonds, 428 residues, 1 model selected  

> select up

11445 atoms, 11742 bonds, 1419 residues, 1 model selected  

> hide #1 models

> show #1 models

> hide sel cartoons

> select clear

Drag select of 213 atoms, 43 residues  

> select up

398 atoms, 404 bonds, 47 residues, 1 model selected  

> select up

767 atoms, 783 bonds, 93 residues, 1 model selected  

> hide sel atoms

> hide sel surfaces

> hide sel cartoons

> select clear

Drag select of 43 atoms, 9 residues  

> select up

208 atoms, 216 bonds, 25 residues, 1 model selected  

> select up

1023 atoms, 1049 bonds, 125 residues, 1 model selected  

> hide sel atoms

> select clear

Drag select of 3 residues  

> select up

73 atoms, 77 bonds, 8 residues, 1 model selected  

> select up

1023 atoms, 1049 bonds, 125 residues, 1 model selected  

> hide sel cartoons

> select clear

Drag select of 3509 atoms, 3348 bonds  

> select up

5955 atoms, 5881 bonds, 550 residues, 1 model selected  

> show sel atoms

> select clear

Drag select of 358 atoms, 370 bonds  

> select clear

Drag select of 218 atoms, 226 bonds  
Drag select of 274 atoms, 277 bonds  

> select up

505 atoms, 507 bonds, 73 residues, 1 model selected  

> select up

567 atoms, 575 bonds, 73 residues, 1 model selected  

> select up

2322 atoms, 2376 bonds, 285 residues, 1 model selected  

> hide sel atoms

> select clear

Drag select of 32 atoms, 32 bonds  

> select up

36 atoms, 32 bonds, 7 residues, 1 model selected  

> select up

51 atoms, 50 bonds, 7 residues, 1 model selected  

> select up

159 atoms, 159 bonds, 22 residues, 1 model selected  

> select protein

12468 atoms, 12791 bonds, 1544 residues, 1 model selected  

> hide sel atoms

Drag select of 2700 atoms, 2550 bonds  

> contacts sel restrict both resSeparation 8 interModel false intraMol false
> ignoreHiddenModels true select true color #c349c3 dashes 0 radius 0.05
> reveal true log true
    
    
    Allowed overlap: -0.4
    H-bond overlap reduction: 0.4
    Ignore contacts between atoms separated by 4 bonds or less
    Ignore contacts between atoms in residues less than 8 apart in sequence
    Detect intra-residue contacts: False
    Detect intra-molecule contacts: False
    
    3359 contacts
        atom1          atom2      overlap  distance
    /M OLA 1 C18   /GB PLM 1 CG    2.142    1.618
[deleted to fit within ticket limits]
    /EC PLM 1 CG   /FA OLA 1 C17   -0.400    4.040
    

  
3359 contacts  
Drag select of 2700 atoms, 2550 bonds, 3359 pseudobonds  

> ui tool show Clashes

> clashes sel restrict both interModel false select true log true
    
    
    Allowed overlap: 0.6
    H-bond overlap reduction: 0.4
    Ignore clashes between atoms separated by 4 bonds or less
    Detect intra-residue clashes: False
    Detect intra-molecule clashes: True
    
    180 clashes
        atom1          atom2      overlap  distance
    /M OLA 1 C18   /GB PLM 1 CG    2.142    1.618
[deleted to fit within ticket limits]
    /IC PLM 1 CG   /KC PLM 1 CF    0.601    3.159
    

  
180 clashes  

> select clear

> close #1.1-2

> select clear

> show cartoons

> color bypolymer

> rainbow


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

Log:
UCSF ChimeraX version: 1.9.dev202405110020 (2024-05-11)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/pcarlton/Downloads/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23/fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_4.cif

Chain information for
fold_mjl_1_50xoleic_palmitic_myristic_sun_1_s8p_x3_2024_05_20_12_23_model_4.cif
#1  
---  
Chain | Description  
A | .  
B C D | .  
  




OpenGL version: 4.1 ATI-4.8.101
OpenGL renderer: AMD Radeon R9 M380 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.3
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: iMac
      Model Identifier: iMac17,1
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 3.2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Memory: 32 GB
      System Firmware Version: 522.0.0.0.0
      OS Loader Version: 540.120.3~37
      SMC Version (system): 2.33f12

Software:

    System Software Overview:

      System Version: macOS 12.7.1 (21G920)
      Kernel Version: Darwin 21.6.0
      Time since boot: 19 days 23:36

Graphics/Displays:

    AMD Radeon R9 M380:

      Chipset Model: AMD Radeon R9 M380
      Type: GPU
      Bus: PCIe
      PCIe Lane Width: x16
      VRAM (Total): 2 GB
      Vendor: AMD (0x1002)
      Device ID: 0x6640
      Revision ID: 0x0080
      ROM Revision: 113-C6005R-800
      VBIOS Version: 113-C6005T-009
      EFI Driver Version: 01.00.800
      Metal Family: Supported, Metal GPUFamily macOS 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: No
          Connection Type: Internal
        EV2336W:
          Resolution: 1080 x 1920
          UI Looks like: 1080 x 1920
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: 80101073
          Mirror: Off
          Online: Yes
          Rotation: 90


Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    appnope: 0.1.4
    asttokens: 2.4.1
    Babel: 2.15.0
    beautifulsoup4: 4.12.3
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 1.2.1
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.17
    ChimeraX-AddH: 2.2.6
    ChimeraX-AlignmentAlgorithms: 2.0.2
    ChimeraX-AlignmentHdrs: 3.5
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.58
    ChimeraX-AtomicLibrary: 14.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.4
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.4.6
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.12.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.3
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.4
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.4
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.4
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.6
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.9.dev202405110020
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.3
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2.1
    ChimeraX-DiffPlot: 1.0
    ChimeraX-DistMonitor: 1.4.2
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    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: 1.1.9
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.2
    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: 2.1.3
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.7
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.14.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.15
    ChimeraX-ModelPanel: 1.5
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NMRSTAR: 1.0.2
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.4
    ChimeraX-PDB: 2.7.5
    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: 1.1.1
    ChimeraX-PubChem: 2.2
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.4.1
    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-Segmentations: 1.3.3
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.3
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.16.4
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.2.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.5
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.39.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.4.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.4
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.2
    contourpy: 1.2.1
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 3.0.10
    debugpy: 1.8.1
    decorator: 5.1.1
    docutils: 0.20.1
    executing: 2.0.1
    filelock: 3.13.4
    fonttools: 4.51.0
    funcparserlib: 2.0.0a0
    glfw: 2.7.0
    grako: 3.16.5
    h5py: 3.11.0
    html2text: 2024.2.26
    idna: 3.7
    ihm: 1.0
    imagecodecs: 2024.1.1
    imagesize: 1.4.1
    ipykernel: 6.29.2
    ipython: 8.21.0
    ipywidgets: 8.1.2
    jedi: 0.19.1
    jinja2: 3.1.4
    jupyter-client: 8.6.0
    jupyter-core: 5.7.2
    jupyterlab-widgets: 3.0.10
    kiwisolver: 1.4.5
    line-profiler: 4.1.2
    lxml: 5.2.1
    lz4: 4.3.3
    MarkupSafe: 2.1.5
    matplotlib: 3.8.4
    matplotlib-inline: 0.1.7
    msgpack: 1.0.8
    nest-asyncio: 1.6.0
    netCDF4: 1.6.5
    networkx: 3.3
    nibabel: 5.2.0
    nptyping: 2.5.0
    numexpr: 2.10.0
    numpy: 1.26.4
    openvr: 1.26.701
    packaging: 23.2
    ParmEd: 4.2.2
    parso: 0.8.4
    pep517: 0.13.1
    pexpect: 4.9.0
    pillow: 10.3.0
    pip: 24.0
    pkginfo: 1.10.0
    platformdirs: 4.2.1
    prompt-toolkit: 3.0.43
    psutil: 5.9.8
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.8
    pydicom: 2.4.4
    pygments: 2.17.2
    pynmrstar: 3.3.4
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.3401
    pyparsing: 3.1.2
    pyproject-hooks: 1.1.0
    PyQt6-commercial: 6.6.1
    PyQt6-Qt6: 6.6.3
    PyQt6-sip: 13.6.0
    PyQt6-WebEngine-commercial: 6.6.0
    PyQt6-WebEngine-Qt6: 6.6.3
    python-dateutil: 2.9.0.post0
    pytz: 2024.1
    pyzmq: 26.0.3
    qtconsole: 5.5.1
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.13.0
    setuptools: 69.5.1
    setuptools-scm: 8.0.4
    sfftk-rw: 0.8.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 7.2.6
    sphinx-autodoc-typehints: 2.0.1
    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: 0.6.3
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2024.1.30
    tinyarray: 1.2.4
    tornado: 6.4
    traitlets: 5.14.2
    typing-extensions: 4.11.0
    tzdata: 2024.1
    urllib3: 2.2.1
    wcwidth: 0.2.13
    webcolors: 1.13
    wheel: 0.43.0
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.10

Change History (2)

comment:1 by Eric Pettersen, 17 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
Description: modified (diff)
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in garbage collection

comment:2 by Eric Pettersen, 17 months ago

Resolution: → duplicate
Status: accepted → closed

Hi Peter,

Thanks for reporting this problem. It is fixed in the 1.8 release candidate (or the 1.9 daily build that you are currently using), so as long as you aren't using the 1.7.1 release then this crash should not affect you anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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