ChimeraX closed when loading ISOLDE demo file

[kdttruc83@…]

The following bug report has been submitted:
Platform:        Linux-4.4.0-154-generic-x86_64-with-debian-stretch-sid
ChimeraX Version: 0.91 (2019-07-02)
Description
ChimeraX closed when loading ISOLDE demo file.

Log:
Startup Messages  
---  
warning | 'clip' is a prefix of an existing command 'clipper'  
  
UCSF ChimeraX version: 0.91 (2019-07-02)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show ISOLDE

> set selectionWidth 4

Done loading forcefield  




OpenGL version: 3.3 (Core Profile) Mesa 18.0.5
OpenGL renderer: Mesa DRI Intel(R) Haswell Mobile 
OpenGL vendor: Intel Open Source Technology Center

[Tristan Croll]

Just wondering: is this reproducible on your machine, or does it just happen once. Do you get any sort of traceback in the shell after ChimeraX closes?

[kdttruc83@…]

Hello,
Yes, it happens anytime I load the demo file. Below is what I got from my
terminal.
-----------------------------------------------------------------------------
kimtruc@kimtruc-GL552JX:~$ chimerax-daily
Attribute Qt::AA_ShareOpenGLContexts must be set before QCoreApplication is
created.
WARNING: 'clip' is a prefix of an existing command 'clipper'
Fatal Python error: Segmentation fault

Thread 0x00007fd957fff700 (most recent call first):
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/openmm/forcefields.py",
line 60 in _background_load_ff
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/concurrent/futures/thread.py",
line 57 in run
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/concurrent/futures/thread.py",
line 80 in _worker
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line 865
in run
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line 917
in _bootstrap_inner
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/threading.py", line 885
in _bootstrap

Current thread 0x00007fd99bc75700 (most recent call first):
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/molobject.py",
line 1379 in get_rotamers
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/validation/rota_annotation.py",
line 110 in track_whole_model
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/graphics/drawing.py",
line 243 in __setattr__
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/validation/rota_annotation.py",
line 75 in __init__
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/session_extensions.py",
line 223 in get_rota_annotator
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/isolde.py",
line 2441 in _change_selected_model
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/isolde.py",
line 998 in _update_model_list
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 130 in invoke
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 190 in activate
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 325 in activate_trigger
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py",
line 482 in add
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/clipper/symmetry.py",
line 154 in get_symmetry_handler
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/isolde.py",
line 2427 in _change_selected_model
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/isolde.py",
line 998 in _update_model_list
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 130 in invoke
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 190 in activate
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/triggerset.py",
line 325 in activate_trigger
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py",
line 482 in add
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/models.py",
line 628 in open
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/core/commands/open.py",
line 68 in open
  File
"/home/kimtruc/.local/share/ChimeraX/0.91/site-packages/chimerax/isolde/isolde.py",
line 3288 in load_demo_data
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/chimerax/ui/gui.py",
line 254 in event_loop
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py",
line 745 in init
  File
"/usr/lib/ucsf-chimerax-daily/lib/python3.7/site-packages/ChimeraX_main.py",
line 869 in <module>
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/runpy.py", line 85 in
_run_code
  File "/usr/lib/ucsf-chimerax-daily/lib/python3.7/runpy.py", line 193 in
_run_module_as_main
Segmentation fault (core dumped)
----------------------------------------------------------------------------------

Best regards,


*Truc Kim*Structural Biology Laboratory
Department of Molecular Cell Biology
Sungkyunkwan University School of Medicine
Suwon City 440-746, South Korea
Tel: +82-31-299-6150
Fax: +82-31-299-6159
Email: kdttruc83@gmail.com


Vào Th 7, 13 thg 7, 2019 vào lúc 00:54 ChimeraX <
ChimeraX-bugs-admin@cgl.ucsf.edu> đã viết:

[tic20@…]

Ah. From the directories, it looks like you’re using one of the Ubuntu ChimeraX packages? I’m afraid ISOLDE isn’t currently compatible with those due to their using a different compiler version. You’ll need to use the “Generic Linux” version of ChimeraX instead. You shouldn’t actually have to reinstall ISOLDE - just download the generic Linux ChimeraX tarball, extract to a directory of your choice, and run ChimeraX from the executable in its bin directory. It uses the same directories for the Tool Shed, so ISOLDE should be there ready to go.
 

 

[Tristan Croll]

Cleaning up old tickets. The problem of ISOLDE/Clipper not working with Ubuntu builds is not one I can currently address - that would require the ChimeraX Tool Shed to support separate bundle builds for different Linux flavours. For now, the solution remains to use the "Generic Linux" build of ChimeraX if you want to use ISOLDE.