Crash opening mmCIF file

[jan.binovsky@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-172-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.8.dev202403120048 (2024-03-12 00:48:54 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Current thread 0x00007f0a822be740 (most recent call first):
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/mmcif/__init__.py", line 54 in open
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 484 in remember_data_format
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 513 in collated_open
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 213 in provider_open
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/open_command/cmd.py", line 131 in cmd_open
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/core/commands/cli.py", line 2904 in run
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/core/commands/run.py", line 49 in run
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/open_command/dialog.py", line 334 in _qt_safe
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/ui/gui.py", line 280 in event_loop
  File "/cemcofsw/em/chimerax/daily-2024.03.12/lib/python3.11/site-packages/chimerax/core/__main__.py", line 918 in init
  File "/cemcofsw/em/chimerax/daily-2024.03.12/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.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, 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, lxml._elementpath, lxml.etree, 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, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif (total: 51)
===== Log before crash start =====
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  

still retrieving bundle list from toolshed  

> isolde shorthand

Error running startup command 'isolde shorthand': Unknown command: isolde
shorthand  
UCSF ChimeraX version: 1.8.dev202403120048 (2024-03-12)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /home/janbinovsky/Projects/baseplate_building_phi812/baseplate/native_structures/native_complete/phenix_native_complete/PreparePDBDeposition_24/nat_complete_rsr022_third_repaired_assembly_deposit.cif


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

Log:
> isolde shorthand

isolde is provided by the uninstalled bundle ISOLDE versions 1.7rc1 – 1.7.1  

> lighting soft

> hide atoms

> show cartoons

> mousemode shift middleMode center

UCSF ChimeraX version: 1.8.dev202403120048 (2024-03-12)  
© 2016-2024 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 3.3.0 NVIDIA 470.239.06
OpenGL renderer: NVIDIA GeForce RTX 3090/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.11.4
Locale: en_US.UTF-8
Qt version: PyQt6 6.6.1, Qt 6.6.1
Qt runtime version: 6.6.2
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=xubuntu
XDG_SESSION_DESKTOP=xubuntu
XDG_CURRENT_DESKTOP=XFCE
DISPLAY=:0.0
Manufacturer: M Computers s.r.o.
Model: Super Server
OS: Ubuntu 20.04 Focal Fossa
Architecture: 64bit ELF
Virtual Machine: none
CPU: 32 AMD EPYC 7302P 16-Core Processor
Cache Size: 512 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:          251Gi        19Gi       230Gi       330Mi       2.2Gi       230Gi
	Swap:            0B          0B          0B

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation Device [10de:2204] (rev a1)	
	Subsystem: Gigabyte Technology Co., Ltd Device [1458:403b]	
	Kernel driver in use: nvidia

Installed Packages:
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[Greg Couch]

My humble apologies for not getting back to you sooner.

Do you still have the mmCIF file or any mmCIF file that fails to open in ChimeraX? If so, please share it with us. I have seen this bug many times, but have not been able to reproduce it yet.

In the bug report the file is /home/janbinovsky/Projects/baseplate_building_phi812/baseplate/native_structures/native_complete/phenix_native_complete/PreparePDBDeposition_24/nat_complete_rsr022_third_repaired_assembly_deposit.cif

[jan.binovsky@…]

Dear Greg,

no worries. I can provide some context, if it helps.

I performed real_space_refine in Phenix with a symmetrized model (C3 
symmetry). Then, I saved only 1/3 of that model using ChimeraX chain 
selection and proceeded with prepare_pdb_deposition in Phenix. Looking 
at the job history in Phenix, I see 7 different prepare_pdb_deposition 
jobs, in which I tried to modify my model.cif. All but the last job 
output model triggers the ChimeraX crash. I don't remember changes I 
made but I will provide to you with the .cif from the bug report, then 
the last modified .cif that triggers the crash and the first .cif that 
doesn't trigger the crash. I am using my university file depository - 
let me know if you have problems accessing the files.

Model from the bug report: https://is.muni.cz/go/hng79d
Last model causing crash: https://is.muni.cz/go/t5a3vs
First model not causing crash: https://is.muni.cz/go/fyl0pn

Best regards,
Jan


On 18. 04. 25 7:38, ChimeraX wrote:
>
>
>

smime.p7s​

[jan.binovsky@…]

Added by email2trac

[Greg Couch]

Unfortunately, I can not access those files. My computer can reach the website, but get a "Zkuste později" 503 error.

[jan.binovsky@…]

Dear Greg,

please find a zipped files attached.

Jan

On 22. 04. 25 9:45, ChimeraX wrote:
>

files_ticket14761_export.zip​

smime-1.p7s​

[jan.binovsky@…]

Added by email2trac

[jan.binovsky@…]

Added by email2trac

[Greg Couch]

Many thanks for the mmCIF files. What software wrote those files? There are lots of unexpected duplicate entries in the mmCIF tables related to entities: entity, entity_poly, and entity_poly_seq. In particular, ChimeraX is getting confused because of the duplicates in the entity_poly_seq table. I'll add code to protect against those errors.

[jan.binovsky@…]

Dear Greg,

those files are outputs of the tool /mmtbx.prepare_pdb_deposition/ (link 
<https://phenix-online.org/documentation/reference/prepare_pdb_deposition.html>) 
as a part of the Phenix model refinement package. Thank you for your 
work to make ChimeraX better!

Best regards,
Jan

On 22. 04. 25 19:57, ChimeraX wrote:
>

smime-2.p7s​

[jan.binovsky@…]

Added by email2trac

[Greg Couch]

Thanks again for the wonderfully bad mmCIF files. In addition to the previously noted errors, it turns out that the sequence information didn't match the atom information. The current ChimeraX daily build doesn't crash, gives warnings for the problems it finds, and does a better job of connecting the residues. If the current version of the Phenix deposition tool makes the same mistakes, you should file a bug with them.