![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
#14506 closed defect (fixed)
Crash in garbage collection
| Reported by: | Owned by: | pett | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Core | Version: | |
| Keywords: | Cc: | Tom Goddard, Greg Couch | |
| Blocked By: | Blocking: | ||
| Notify when closed: | yakonfire@yahoo.com | Platform: | all |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.2.1-arm64-arm-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: Bus error
Thread 0x000000030363f000 (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
Thread 0x0000000302633000 (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 0x00000001d80dd000 (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/atomic/molarray.py", line 161 in
File "/Applications/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 "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 774 in _find_acceptors
File "/Applications/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 "/Applications/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 "/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/cli.py", line 3468 in __call__
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 2929 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/core/scripting.py", line 184 in _run_commands
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py", line 61 in run_command_script
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/runscript.py", line 51 in runscript
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/cmd_line/tool.py", line 319 in execute
File "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/cmd_line/tool.py", line 146 in keyPressEvent
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.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, PIL._imagingmath, 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, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp, chimerax.mlp._mlp (total: 57)
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"procExitAbsTime" : 981446682657,
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"procPath" : "\/Applications\/ChimeraX-1.7.1.app\/Contents\/MacOS\/ChimeraX",
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"codeSigningTeamID" : "LWV8X224YF",
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"termination" : {"flags":0,"code":10,"namespace":"SIGNAL","indicator":"Bus error: 10","byProc":"ChimeraX","byPid":687},
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===== Log before crash start =====
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
> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc
> alias picmovie view orient ; save "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4"
> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb" ; alphafold pae
> #1 file "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W173
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W173/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
4 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W173/W173_contacts_hbonds.jpg"
> supersample 2
Cannot save '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W173/W173_contacts_hbonds.jpg':
[Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W173/W173_contacts_hbonds.jpg'
> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc
> alias picmovie view orient ; save "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4"
> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb" ; alphafold pae
> #1 file "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W181
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
4 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg"
> supersample 2
Cannot save '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg':
[Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg'
> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc
> alias picmovie view orient ; save "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4"
> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb" ; alphafold pae
> #1 file "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W181
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
4 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg"
> supersample 2
Cannot save '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg':
[Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg'
> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc
> alias picmovie view orient ; save "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4"
> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb" ; alphafold pae
> #1 file "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W181
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
4 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg"
> supersample 2
Cannot save '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg':
[Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg'
> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc
> alias picmovie view orient ; save "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4"
> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb" ; alphafold pae
> #1 file "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults W181
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
4 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg"
> supersample 2
Cannot save '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg':
[Errno 70] Stale NFS file handle: '/Users/neyrinck/Google Drive/My
Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults/W181/W181_contacts_hbonds.jpg'
> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc
> alias picmovie view orient ; save "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4"
> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb" ; alphafold pae
> #1 file "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> AF122
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/best_model.pdb"
Cannot open files: [Errno 60] Operation timed out
> runscript /Users/neyrinck/Dropbox/notebook/proteins/makepictures.cxc
> alias picmovie view orient ; save "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3.jpg" supersample 2 ; movie record ; turn y 2 180 ; wait
> 180 ; movie encode "/Users/neyrinck/Google Drive/My
> Drive/$1/$2/$2_$3_rot.mp4"
> alias makepicture close ; set bgColor white ; windowsize 480 480 ;open
> "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model.pdb" ; alphafold pae
> #1 file "/Users/neyrinck/Google Drive/My Drive/$1/$2/best_model_pae.json" ;
> view orient ; sequence chain #1/A ; sequence chain #1/B ;color bychain ;
> color /A indianred ; color /B royalblue ; alphafold contacts /A to /B
> palette paegreen ; hbonds /A reveal true restrict /B color fuchsia radius
> 0.8 dashes 2 ; picmovie $1 $2 contacts_hbonds ; style sphere ; show atoms ;
> picmovie $1 $2 sphere ; style nucleic stick ; hide atoms ; coulombic key
> true ; picmovie $1 $2 coulombic ; style nucleic stick ; hide atoms ; mlp key
> true ; picmovie $1 $2 hydrophobic
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> AF122
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
5 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/AF122_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AF122/AF122_contacts_hbonds_rot.mp4
Changed 8618 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/AF122_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AF122/AF122_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -24.67, mean
-4.45, maximum 15.72
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.64, mean
-0.38, maximum 11.56
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/AF122_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AF122/AF122_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -27.89, mean
-5.06, maximum 23.83
Map values for surface "best_model.pdb_B SES surface": minimum -28.22, mean
-4.673, maximum 23.95
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF122/AF122_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AF122/AF122_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> AF182
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
10 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/AF182_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AF182/AF182_contacts_hbonds_rot.mp4
Changed 7870 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/AF182_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AF182/AF182_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -25.41, mean
-4.28, maximum 18.51
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -21.53, mean
-2.50, maximum 8.95
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/AF182_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AF182/AF182_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -30.69, mean
-5.172, maximum 25.37
Map values for surface "best_model.pdb_B SES surface": minimum -28.23, mean
-5.938, maximum 21.78
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AF182/AF182_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AF182/AF182_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> AG123
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
1 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/AG123_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG123/AG123_contacts_hbonds_rot.mp4
Changed 8313 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/AG123_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG123/AG123_sphere_rot.mp4
Changed 0 atom styles
Exception ignored in tp_clear of:
Traceback (most recent call last):
File
"/Applications/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
self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers]
^^^^^^^^^^^^^^^^^^^^^
TypeError: NoneType takes no arguments
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -18.51, mean
-0.84, maximum 14.74
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.17, mean
-0.75, maximum 13.58
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/AG123_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG123/AG123_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -30.62, mean
-6.387, maximum 26.65
Map values for surface "best_model.pdb_B SES surface": minimum -27.46, mean
-1.412, maximum 24.61
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG123/AG123_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG123/AG123_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> AG172
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
1 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/AG172_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG172/AG172_contacts_hbonds_rot.mp4
Changed 7440 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/AG172_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG172/AG172_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.63, mean
-0.66, maximum 13.56
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -11.30, mean
-0.42, maximum 13.19
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/AG172_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG172/AG172_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -30.18, mean
-6.405, maximum 25.47
Map values for surface "best_model.pdb_B SES surface": minimum -27.92, mean
-1.069, maximum 22.69
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG172/AG172_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG172/AG172_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> AG185
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
21 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/AG185_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG185/AG185_contacts_hbonds_rot.mp4
Changed 8884 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/AG185_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG185/AG185_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.18, mean
-1.04, maximum 24.85
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -13.87, mean
0.51, maximum 20.70
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/AG185_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG185/AG185_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -31.84, mean
-6.422, maximum 27.62
Map values for surface "best_model.pdb_B SES surface": minimum -28.14, mean
-5.46, maximum 22.87
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/AG185/AG185_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../AG185/AG185_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> T123
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
2 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/T123_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T123/T123_contacts_hbonds_rot.mp4
Changed 3522 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/T123_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T123/T123_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.06, mean
-2.88, maximum 11.81
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -14.95, mean
-0.67, maximum 14.16
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/T123_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T123/T123_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -25.56, mean
-5.424, maximum 22.49
Map values for surface "best_model.pdb_B SES surface": minimum -30.2, mean
-1.372, maximum 24.34
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T123/T123_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T123/T123_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> T128
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
Exception ignored in tp_clear of:
Traceback (most recent call last):
File
"/Applications/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
self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers]
^^^^^^^^^^^^^^^^^^^^^
TypeError: NoneType takes no arguments
0 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/T128_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T128/T128_contacts_hbonds_rot.mp4
Changed 4102 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/T128_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T128/T128_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -18.14, mean
-3.19, maximum 12.44
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -13.21, mean
1.95, maximum 21.27
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/T128_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T128/T128_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -25.49, mean
-5.152, maximum 22.32
Map values for surface "best_model.pdb_B SES surface": minimum -26.95, mean
-1.046, maximum 24.12
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/T128/T128_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../T128/T128_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> U110
> key lipophilicity :-20 :0 :20 white: white: white: white: white: white:
> white: white: white: white:
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
0 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/U110_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U110/U110_contacts_hbonds_rot.mp4
Changed 671 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/U110_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U110/U110_sphere_rot.mp4
Changed 0 atom styles
Exception ignored in tp_clear of:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/grako/ast.py", line 59, in update
def upairs(d):
TypeError: NoneType takes no arguments
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -16.21, mean
-5.66, maximum 8.34
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -11.94, mean
-1.25, maximum 8.75
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/U110_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U110/U110_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -24.43, mean
-4.109, maximum 24.15
Map values for surface "best_model.pdb_B SES surface": minimum -22.87, mean
-3.776, maximum 25.35
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U110/U110_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U110/U110_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> U126
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
3 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/U126_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U126/U126_contacts_hbonds_rot.mp4
Changed 3648 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/U126_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U126/U126_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.88, mean
-5.58, maximum 10.28
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.59, mean
0.10, maximum 12.63
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/U126_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U126/U126_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -25.53, mean
-4.704, maximum 23.87
Map values for surface "best_model.pdb_B SES surface": minimum -29.31, mean
-4.227, maximum 23.19
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U126/U126_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U126/U126_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> U127
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
11 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/U127_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U127/U127_contacts_hbonds_rot.mp4
Changed 3769 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/U127_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U127/U127_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -25.55, mean
-7.54, maximum 9.34
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -15.49, mean
-1.52, maximum 18.02
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/U127_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U127/U127_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -29.54, mean
-4.686, maximum 21.33
Map values for surface "best_model.pdb_B SES surface": minimum -29.63, mean
-5.687, maximum 23.3
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U127/U127_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U127/U127_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> U168
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
Exception ignored in tp_clear of:
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/geometry/matrix.py", line 33, in apply_matrix
r = matrix_multiply(points, transpose(tf[:, :3]))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
TypeError: NoneType takes no arguments
8 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/U168_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U168/U168_contacts_hbonds_rot.mp4
Changed 7517 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/U168_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U168/U168_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -26.29, mean
-6.88, maximum 11.42
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -27.34, mean
-3.20, maximum 11.62
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/U168_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U168/U168_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -29.78, mean
-4.178, maximum 24.02
Map values for surface "best_model.pdb_B SES surface": minimum -28.65, mean
-5.09, maximum 23.77
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U168/U168_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U168/U168_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> U181
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
5 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/U181_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U181/U181_contacts_hbonds_rot.mp4
Changed 8811 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/U181_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U181/U181_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.51, mean
-5.36, maximum 10.83
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -22.93, mean
-0.07, maximum 18.91
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/U181_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U181/U181_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -24.06, mean
-3.834, maximum 20.12
Map values for surface "best_model.pdb_B SES surface": minimum -28.14, mean
-3.16, maximum 24.29
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/U181/U181_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../U181/U181_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> V139
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
13 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/V139_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V139/V139_contacts_hbonds_rot.mp4
Changed 6417 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/V139_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V139/V139_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -15.63, mean
-1.93, maximum 18.79
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -19.55, mean
-2.60, maximum 11.98
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/V139_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V139/V139_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -30.7, mean
-5.511, maximum 22.83
Map values for surface "best_model.pdb_B SES surface": minimum -30.93, mean
-5.365, maximum 24.34
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V139/V139_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V139/V139_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> V142
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
6 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/V142_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V142/V142_contacts_hbonds_rot.mp4
Changed 7491 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/V142_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V142/V142_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.17, mean
-1.14, maximum 17.41
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -17.17, mean
1.17, maximum 20.04
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/V142_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V142/V142_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -27.59, mean
-5.329, maximum 21.93
Map values for surface "best_model.pdb_B SES surface": minimum -30.22, mean
-3.754, maximum 24.74
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V142/V142_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V142/V142_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> V143
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
11 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/V143_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V143/V143_contacts_hbonds_rot.mp4
Changed 7562 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/V143_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V143/V143_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -17.31, mean
-1.24, maximum 18.49
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.42, mean
0.45, maximum 19.37
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/V143_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V143/V143_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -28.81, mean
-5.284, maximum 21.46
Map values for surface "best_model.pdb_B SES surface": minimum -30.01, mean
-3.498, maximum 25.47
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V143/V143_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V143/V143_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> V173
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
5 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/V173_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V173/V173_contacts_hbonds_rot.mp4
Changed 6995 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/V173_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V173/V173_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.55, mean
-2.48, maximum 17.12
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.14, mean
-0.35, maximum 17.74
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/V173_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V173/V173_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -24.15, mean
-4.967, maximum 27.85
Map values for surface "best_model.pdb_B SES surface": minimum -32.62, mean
-4.467, maximum 25.2
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V173/V173_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V173/V173_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> V181
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
1 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/V181_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V181/V181_contacts_hbonds_rot.mp4
Changed 9108 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/V181_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V181/V181_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.93, mean
-1.17, maximum 16.60
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.19, mean
-0.13, maximum 16.80
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/V181_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V181/V181_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -26.24, mean
-5.43, maximum 22.03
Map values for surface "best_model.pdb_B SES surface": minimum -29.84, mean
-3.222, maximum 27.55
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/V181/V181_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../V181/V181_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> W123
> key lipophilicity :-20 :0 :20 white:
> key darkcyan:-20 white:0 darkgoldenrod:20 white: white:
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
0 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/W123_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W123/W123_contacts_hbonds_rot.mp4
Changed 3494 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/W123_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W123/W123_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -20.12, mean
-3.52, maximum 8.53
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -24.87, mean
-0.67, maximum 11.88
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/W123_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W123/W123_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -27.02, mean
-6.604, maximum 22.22
Map values for surface "best_model.pdb_B SES surface": minimum -27.4, mean
-1.407, maximum 24.07
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W123/W123_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W123/W123_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> W135
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
1 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/W135_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W135/W135_contacts_hbonds_rot.mp4
Changed 4940 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/W135_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W135/W135_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -22.35, mean
-4.28, maximum 8.59
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -23.99, mean
0.69, maximum 17.52
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/W135_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W135/W135_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -33.07, mean
-6.808, maximum 22.97
Map values for surface "best_model.pdb_B SES surface": minimum -29.32, mean
-2.714, maximum 24.53
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W135/W135_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W135/W135_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> W139
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
10 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/W139_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W139/W139_contacts_hbonds_rot.mp4
Changed 6397 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/W139_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W139/W139_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.85, mean
-5.49, maximum 7.56
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -34.76, mean
-2.90, maximum 13.36
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/W139_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W139/W139_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -26.99, mean
-6.956, maximum 22.21
Map values for surface "best_model.pdb_B SES surface": minimum -34.58, mean
-5.318, maximum 23.88
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W139/W139_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W139/W139_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> W142
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
3 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/W142_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W142/W142_contacts_hbonds_rot.mp4
Changed 7471 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/W142_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W142/W142_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -21.38, mean
-4.72, maximum 10.92
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -16.31, mean
1.27, maximum 19.35
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/W142_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W142/W142_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -28.4, mean
-6.661, maximum 21.77
Map values for surface "best_model.pdb_B SES surface": minimum -32.41, mean
-3.752, maximum 24.66
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W142/W142_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W142/W142_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> W143
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
6 hydrogen bonds found
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/W143_contacts_hbonds.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W143/W143_contacts_hbonds_rot.mp4
Changed 7542 atom styles
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/W143_sphere.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W143/W143_sphere_rot.mp4
Changed 0 atom styles
Using Amber 20 recommended default charges and atom types for standard
residues
Coulombic values for best_model.pdb_A SES surface #1.3: minimum, -19.48, mean
-4.31, maximum 10.66
Coulombic values for best_model.pdb_B SES surface #1.4: minimum, -20.19, mean
0.44, maximum 20.10
> key red-white-blue :-10 :0 :10 showTool true
> ui mousemode right "color key"
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/W143_coulombic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W143/W143_coulombic_rot.mp4
Changed 0 atom styles
Map values for surface "best_model.pdb_A SES surface": minimum -34.86, mean
-6.835, maximum 21.92
Map values for surface "best_model.pdb_B SES surface": minimum -29.08, mean
-3.558, maximum 24.54
> key lipophilicity :-20 :0 :20 showTool true
> save "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W143/W143_hydrophobic.jpg"
> supersample 2
Movie saved to /Users/neyrinck/.../W143/W143_hydrophobic_rot.mp4
> makepicture 0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy
> W168
> ui mousemode right translate
> open "/Users/neyrinck/Google Drive/My
> Drive/0_DUF1220_202208_howard/0_AlphaFold_results/0_MarksResults_copy/W168/best_model.pdb"
Chain information for best_model.pdb #1
---
Chain | Description
A | No description available
B | No description available
Alignment identifier is 1/A
Alignment identifier is 1/B
Exception ignored in tp_clear of:
Traceback (most recent call last):
File
"/Applications/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
self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers]
^^^^^^^^^^^^^^^^^^^^^
TypeError: NoneType takes no arguments
===== Log before crash end =====
Log:
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 Metal - 88
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple
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: MacBookPro18,2
Model Number: Z14W00106LL/A
Chip: Apple M1 Max
Total Number of Cores: 10 (8 performance and 2 efficiency)
Memory: 32 GB
System Firmware Version: 10151.61.4
OS Loader Version: 10151.61.4
Software:
System Software Overview:
System Version: macOS 14.2.1 (23C71)
Kernel Version: Darwin 23.2.0
Time since boot: 16 hours, 31 minutes
Graphics/Displays:
Apple M1 Max:
Chipset Model: Apple M1 Max
Type: GPU
Bus: Built-In
Total Number of Cores: 24
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3456 x 2234 Retina
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-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
Attachments (5)
Change History (25)
comment:1 by , 21 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 , 21 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
comment:3 by , 21 months ago
| Notify when closed: | → yakonfire@yahoo.com |
|---|---|
| Reporter: | changed from to |
I changed the reporter to Eric so we can discuss this further without spamming the original reporter with details they won't understand.
comment:4 by , 21 months ago
Eric wrote:
Note that this ticket has something interesting at the end:
Exception ignored in tp_clear of: Traceback (most recent call last): File "/Applications/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 self._object_list = [c.c_ptr_to_py_inst(p) for p in self._pointers] ^^^^^^^^^^^^^^^^^^^^^ TypeError: NoneType takes no arguments
My Google-fu didn't uncover anything incredibly helpful in regards to that error message, but maybe your Google-fu is better. That code is in the iter method for a Collection. Seems like something is iterating over a Collection that has been garbage collected -- which does correspond to the Python backtrace:
File "/Applications/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 "/Applications/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 "/Applications/ChimeraX-1.7.1.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/hbonds/hbond.py", line 774 in _find_acceptors File "/Applications/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
I dunno, still confusing.
comment:5 by , 21 months ago
This does seem like a possible clue.
First there is the "Exception ignored in tp_clear of: ". According to Python docs, tp_clear is a type object method that breaks reference cycles during cyclic garbage collection:
https://docs.python.org/3/c-api/typeobj.html#c.PyTypeObject.tp_clear
I guess that is not too surprising since we get a garbage collection crash later. But it seems that this warning detected a serious problem in a previous round of garbage collection and ignored it. That message is supposed to have the name of the type after the ":" and why it doesn't name any type is mysterious. No other ChimeraX bug report contains the word tp_clear.
Then there is the Python one-line traceback with "TypeError: NoneType takes no arguments". I don't think that is part of the previous tp_clear warning. And the NoneType takes no arguments appears to mean c.c_ptr_to_py_inst is None. This appears to be in an Atoms collection coming from hbonds and c = Atoms._object_class so c = Atom. So if I read this right it means Atom.c_ptr_to_py_inst is None, the class attribute is None. The c_ptr_to_py_inst method is defined in cymol.pyx as a member of CyAtom. How could it be None? Cython generated the CyAtom type. It seems like either Atom no longer has CyAtom as a base class or the CyAtom class has been cleaned up. None of that seems plausible. The Atoms collection is holding a reference to the Atom class.
I'm baffled. The one glimmer I get from this is that maybe our Cython wrapping of CyAtom is involved in these garbage collection crashes.
comment:6 by , 21 months ago
Hmm... I tried calling None as if it were a function and it does not say "NoneType takes no argumensts", it says NoneType object is not callable.
>>> x = None >>> x(1) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: 'NoneType' object is not callable
To get the reported error I have to call the NoneType constructor with an argument
>>> t = None.__class__ >>> t <class 'NoneType'> >>> t(1) Traceback (most recent call last): File "<stdin>", line 1, in <module> TypeError: NoneType takes no arguments
That makes it looks like c.c_ptr_to_py_inst is not None, it is NoneType.
Maybe more plausible is that c_ptr_to_py_inst() is trying to create a Python instance and that code due to some error calls the NoneType constructor with an argument.
I guess my only thought is still that Cython is somehow the culprit. It appears that ChimeraX 1.7 has the same Cython version 0.29.33 (changed Jan 2023) as ChimeraX 1.6. So a change in Cython version does not seem to be the cause.
comment:7 by , 21 months ago
The atomic_lib C++ code py_instance() creates an instance (in our PythonInstance.instantiate.h file) using
PyObject* py_inst = PyObject_CallFunctionObjArgs(class_inst, py_ptr, nullptr);
apparently calling the class constructor with one argument. So if somehow class_inst was NoneType that would explain the reported error. It appears that code would then throw a C++ runtime exception with an error message "Cannot construct python instance ..." which we did not see.
Who knows.
comment:8 by , 21 months ago
I think by Occam's Razor it's more likely that c.c_ptr_to_py_inst is NoneType, though I have no idea how that would happen.
comment:9 by , 21 months ago
In your study of the garbage collection crash tickets was there ever a case where it crashed without opening an atomic model? for example a session with only volumes?
comment:11 by , 21 months ago
Working off the shortest reported ticket (#10422), I have a minimal script that crashes in garbage collection a large fraction of the time. I'm currently working on binary search of the code the script calls to try to find the culprit. Stopping for today, but the offending routine seems to be chimerax.std_commands.defattr.defattr(), used by add_charges() (the script calls "coulombic"). I'm attaching the script and the input file it needs.
by , 21 months ago
by , 21 months ago
| Attachment: | AF-A0A0F8XFT2-F1-model_v4.cif added |
|---|
comment:13 by , 21 months ago
| Cc: | added |
|---|
Okay, so my current theory is that there is nothing wrong in that __del__ method per se, though it is necessary for the garbage collector to try to call that __del__ method in order to crash, but it is something earlier that causes the bad state that is actually responsible for the crash.
comment:14 by , 21 months ago
comment:15 by , 21 months ago
I ran a script to look at all Python object seen by the garbage collector and count the number of references to each of those seen by the garbage collector and see if any object has too low a reference count. It found no low reference counts after each step of the gc.py crash test script (run in GUI mode). So I start to doubt the theory that the crash is from a Python object that has too low a reference count. Instead maybe it is a case of memory overwrite.
I attached my reference count checking script test_gc_refcount.py. It takes about 10 minutes when ChimeraX is started in GUI mode to check 180,000 objects.
by , 21 months ago
| Attachment: | test_gc_refcount.py added |
|---|
Python script to look for low reference counts.
comment:16 by , 20 months ago
Attaching a simplified script and the structure it uses, which is just a dipeptide with hydrogens, which means that coulombic does not run addh and does not make a temporary copy of the molecule, eliminating a lot of code paths.
comment:18 by , 20 months ago
| Resolution: | can't reproduce |
|---|---|
| Status: | closed → reopened |
comment:19 by , 20 months ago
| Resolution: | → fixed |
|---|---|
| Status: | reopened → closed |
Fixed the test case. There were two problems. First a little background...
Chains (and StructureSeqs) inherit from Sequence. Since chain sequences may be involved in alignments, their basic Sequence information may be required after the Chain itself is gone. Therefore Chains are not deleted at the same time as their structure is closed -- they are deleted when their reference count goes to zero. So when a structure is closed, its C++ Chain objects directly notify their Python counterparts that they are now essentially Sequences and the Python objects change their __class__ attributes to Sequence.
In the context of this ticket, the obvious first problem is that the demotion from Chain to Sequence frequently happens as the garbage collector is running, and executing Python code while garbage collection is running is a recipe for disaster. The other, less obvious, problem is that, unlike Chimera and Python 2, changing __class__ also seems to lead to crashing, even if that change is not happening directly during garbage collection. __class__ is not read only, and I don't see any admonition in the documentation against changing it, but I'm not going to spit into the wind: I rearchitected my code to not use that methodology.
Fix: https://github.com/RBVI/ChimeraX/commit/d9bf7a93d51f312a6c2a0fd4a3bded069de4a011
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Hi Mark,
--Eric