Opened 15 months ago

Closed 15 months ago

#15613 closed defect (duplicate)

Crash in garbage collection

Reported by: guiolive@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Core Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-6.5.0-41-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.7.1 (2024-01-23 01:58:08 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007ff5957fa640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff595ffb640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff5967fc640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/selectors.py", line 415 in select
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/connection.py", line 930 in wait
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff596ffd640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff5977fe640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff597fff640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff5acb7a640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff5ad37b640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff5adb7c640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff5ae37d640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Thread 0x00007ff5aeb7e640 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.11/multiprocessing/pool.py", line 114 in worker
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 975 in run
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax/lib/python3.11/threading.py", line 995 in _bootstrap

Current thread 0x00007ff6a2862b80 (most recent call first):
  Garbage-collecting
  File "/usr/lib/ucsf-chimerax/lib/python3.11/weakref.py", line 576 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 1613 in remove_deleted_pointers
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 134 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 894 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/molarray.py", line 253 in filter
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 2221 in _bond_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 1188 in first_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 736 in _position_intercepts
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/atomic/structure.py", line 703 in first_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1086 in first_intercept_children
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/drawing.py", line 1069 in first_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/models.py", line 143 in first_intercept
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 863 in picked_object_on_segment
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 831 in picked_object
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 812 in _front_center_point
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 803 in _front_center_cofr
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 735 in _compute_center_of_rotation
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 708 in _get_cofr
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/graphics/view.py", line 1027 in rotate
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py", line 403 in _rotate
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/std_modes.py", line 311 in mouse_drag
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 550 in _dispatch_mouse_event
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/mouse_modes/mousemodes.py", line 651 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/graphics.py", line 61 in event
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/ui/gui.py", line 275 in event_loop
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1069 in 
  File "", line 88 in _run_code
  File "", line 198 in _run_module_as_main

Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtWebChannel, PyQt6.QtNetwork, PyQt6.QtWebEngineCore, PyQt6.QtPrintSupport, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.surface._surface, chimerax.map._map, chimerax.pdb_lib._load_libs, charset_normalizer.md, PIL._imaging, matplotlib._c_internal_utils, matplotlib._path, kiwisolver._cext, matplotlib._image, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.pdb._pdbio, chimerax.atom_search.ast, chimerax.chem_group._chem_group, chimerax.coulombic._esp (total: 54)
===== Log before crash start =====
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
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  

> alphafold fetch P07713

Fetching AlphaFold database settings from
https://www.rbvi.ucsf.edu/chimerax/data/status/alphafold_database3.json  
Chain information for AlphaFold P07713 #1  
---  
Chain | Description | UniProt  
A | Protein decapentaplegic | DECA_DROME 1-588  
  
Color AlphaFold P07713 by residue attribute pLDDT_score  

> show atoms

> hide cartoons

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  

> set bgColor #ffffff00

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  
Alignment identifier is 1/A  

> select /A:1

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

> select /A:1-30

242 atoms, 245 bonds, 30 residues, 1 model selected  

> select /A:23

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

> select /A:1-23

180 atoms, 182 bonds, 23 residues, 1 model selected  

> select /A:320

5 atoms, 4 bonds, 1 residue, 1 model selected  

> select /A:320-324

36 atoms, 35 bonds, 5 residues, 1 model selected  

> select /A:469

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

> select /A:469-588

961 atoms, 986 bonds, 120 residues, 1 model selected  

> color sel black

> select /A:23

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

> select /A:1-23

180 atoms, 182 bonds, 23 residues, 1 model selected  

> color sel black

> ui mousemode right select

> select clear

> hide atoms

> show cartoons

> ui mousemode right translate

> coulombic

Using Amber 20 recommended default charges and atom types for standard
residues  
Coulombic values for AlphaFold P07713_A SES surface #1.1: minimum, -35.50,
mean 1.13, maximum 18.96  
To also show corresponding color key, enter the above coulombic command and
add key true  

> transparency 80

> transparency 40

> ui mousemode right select

Drag select of AlphaFold P07713_A SES surface, 151954 of 770216 triangles, 151
residues  

> select clear

Drag select of AlphaFold P07713_A SES surface, 3089 of 770216 triangles, 13
residues  

> hide sel surfaces

> select clear

> hide surfaces

> close

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.00.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.00.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.00.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.01.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.01.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.01.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.02.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.02.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.02.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.03.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.03.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.03.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.04.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.04.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.04.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.05.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.05.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.05.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.06.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.06.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.06.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.07.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.07.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.07.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.08.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.08.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.08.pdb #9  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116529/model.008.09.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116529/model.008.09.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.09.pdb #10  
---  
Chain | Description  
A | No description available  
  

> close

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.00.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.00.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.00.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.01.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.01.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.01.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.02.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.02.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.02.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.03.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.03.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.03.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.04.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.04.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.04.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.05.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.05.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.05.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.06.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.06.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.06.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.07.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.07.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.07.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.08.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.08.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.08.pdb #9  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116527/model.008.09.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116527/model.008.09.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.09.pdb #10  
---  
Chain | Description  
A | No description available  
  

> close

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.00.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.00.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.00.pdb #1  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.01.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.01.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.01.pdb #2  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.02.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.02.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.02.pdb #3  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.03.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.03.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.03.pdb #4  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.04.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.04.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.04.pdb #5  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.05.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.05.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.05.pdb #6  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.06.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.06.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.06.pdb #7  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.07.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.07.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.07.pdb #8  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.08.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.08.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.08.pdb #9  
---  
Chain | Description  
A | No description available  
  

> open /home/guibarbosa/Desktop/cluspro.1116528/model.008.09.pdb

Summary of feedback from opening
/home/guibarbosa/Desktop/cluspro.1116528/model.008.09.pdb  
---  
warnings | Ignored bad PDB record found on line 2  
REMARK original generated coordinate pdb file  
  
Duplicate atom serial number found: 1  
Duplicate atom serial number found: 2  
Duplicate atom serial number found: 3  
Duplicate atom serial number found: 4  
Duplicate atom serial number found: 5  
74 messages similar to the above omitted  
  
Chain information for model.008.09.pdb #10  
---  
Chain | Description  
A | No description available  
  

> hide #2 models

> hide #3 models

> hide #4 models

> hide #6 models

> hide #5 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

Drag select of 14 atoms, 11 residues, 14 bonds  

> select clear

> ui mousemode right translate

> open 3IRJ format mmcif fromDatabase pdb

3irj title:  
Solution Structure of Heparin dp24 [more info...]  
  

> hide #1 models

> hide #!11 models

> hide #11.1 models

> hide #11.2 models

> hide #11.3 models

> hide #11.5 models

> hide #11.4 models

> hide #11.8 models

> hide #11.7 models

> hide #11.6 models

> hide #11.9 models

> hide #11.10 models

> hide #11.11 models

> hide #11.12 models

> hide #11.13 models

> hide #11.14 models

> hide #11.15 models

> show #11.3 models

> hide #!11 models

> show #1 models

> select ligand

790 atoms, 820 bonds, 10 residues, 10 models selected  

> select ligand

790 atoms, 820 bonds, 10 residues, 10 models selected  

> hide sel & #1 atoms

> show sel & #1 atoms

> hide sel & #1 atoms

> show #2 models

> show #3 models

> show #4 models

> show #5 models

> show #6 models

> show #8 models

> show #7 models

> show #9 models

> show #10 models

> hide #11.3 models

> close #11

> select ligand

790 atoms, 820 bonds, 10 residues, 10 models selected  

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> show sel & #1 atoms

> show #2 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> hide #1 models

> show #1 models

> show #3 models

> show #4 models

> show #5 models

> show #6 models

> show #7 models

> show #8 models

> show #9 models

> show #10 models

> select ligand

790 atoms, 820 bonds, 10 residues, 10 models selected  

> hide sel atoms

> hide #2 models

> hide #3 models

> hide #4 models

> hide #5 models

> hide #6 models

> hide #7 models

> hide #8 models

> hide #9 models

> hide #10 models

> show #2 models


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

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
You can double click a model's Name or ID in the model panel to edit those
fields  
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: 4.6 (Core Profile) Mesa 23.2.1-1ubuntu3.1~22.04.2
OpenGL renderer: Mesa Intel(R) Xe Graphics (TGL GT2)
OpenGL vendor: Intel

Python: 3.11.2
Locale: pt_BR.UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: xcb

XDG_SESSION_TYPE=wayland
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
WAYLAND_DISPLAY=wayland-0
GNOME_SETUP_DISPLAY=:1
DISPLAY=:0
Manufacturer: LENOVO
Model: 82MD
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 8 11th Gen Intel(R) Core(TM) i5-1135G7 @ 2.40GHz
Cache Size: 8192 KB
Memory:
	               total        used        free      shared  buff/cache   available
	Mem:           7.5Gi       3.9Gi       314Mi       978Mi       3.3Gi       2.3Gi
	Swap:          2.0Gi       463Mi       1.5Gi

Graphics:
	0000:00:02.0 VGA compatible controller [0300]: Intel Corporation TigerLake-LP GT2 [Iris Xe Graphics] [8086:9a49] (rev 01)	
	Subsystem: Lenovo TigerLake-LP GT2 [Iris Xe Graphics] [17aa:3f9c]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.16
    appdirs: 1.4.4
    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: 2023.11.17
    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-LinuxSupport: 1.0.1
    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
    distro: 1.7.0
    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: 23.2
    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
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.8
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.6
    sphinxcontrib-htmlhelp: 2.0.5
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.7
    sphinxcontrib-serializinghtml: 1.1.10
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.4
    urllib3: 2.1.0
    wcwidth: 0.2.13
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9

Change History (2)

comment:1 by Eric Pettersen, 15 months ago

Cc: Tom Goddard added
Component: Unassigned → Core
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, 15 months ago

Resolution: → duplicate
Status: accepted → closed

Hi Guilherme,

Thanks for reporting this problem. It has been fixed in the 1.8 release, so if you upgrade to that then you won't run into it anymore.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

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