Opened 3 years ago

Closed 3 years ago

#8184 closed defect (duplicate)

Crash in ses_surface_geometry

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Surface Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.2.1 (2021-05-05 02:17:36 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Windows fatal exception: access violation

Thread 0x000070b4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\gridsurf.py", line 59 in ses_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\atomic\molsurf.py", line 232 in calculate_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 195 in _calculate_surface
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\threadq.py", line 31 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 932 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 890 in _bootstrap

Thread 0x00003bc0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\gridsurf.py", line 64 in ses_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\atomic\molsurf.py", line 232 in calculate_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 195 in _calculate_surface
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\threadq.py", line 31 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 932 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 890 in _bootstrap

Current thread 0x00001b3c (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\gridsurf.py", line 64 in ses_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\atomic\molsurf.py", line 232 in calculate_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 195 in _calculate_surface
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\threadq.py", line 31 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 932 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 890 in _bootstrap

Thread 0x00000f10 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 302 in wait
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\queue.py", line 89 in join
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\threadq.py", line 64 in apply_to_list
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 162 in surface
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2852 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\ui\gui.py", line 1397 in _run_surf_command
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\ui\gui.py", line 1210 in 
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\ChimeraX_main.py", line 1015 in 
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\runpy.py", line 194 in _run_module_as_main
Windows fatal exception: access violation

Current thread 0x000070b4 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\gridsurf.py", line 64 in ses_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\atomic\molsurf.py", line 232 in calculate_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 195 in _calculate_surface
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\threadq.py", line 31 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 932 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 890 in _bootstrap

Thread 0x00003bc0 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\gridsurf.py", line 64 in ses_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\atomic\molsurf.py", line 232 in calculate_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 195 in _calculate_surface
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\threadq.py", line 31 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 932 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 890 in _bootstrap

Thread 0x00001b3c (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\gridsurf.py", line 64 in ses_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\atomic\molsurf.py", line 232 in calculate_surface_geometry
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 195 in _calculate_surface
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\threadq.py", line 31 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 932 in _bootstrap_inner
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 890 in _bootstrap

Thread 0x00000f10 (most recent call first):
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\threading.py", line 302 in wait
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\queue.py", line 89 in join
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\threadq.py", line 64 in apply_to_list
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\surface\surfacecmds.py", line 162 in surface
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\commands\cli.py", line 2852 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\core\commands\run.py", line 36 in run
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\ui\gui.py", line 1397 in _run_surf_command
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\ui\gui.py", line 1210 in 
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\chimerax\ui\gui.py", line 293 in event_loop
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\ChimeraX_main.py", line 866 in init
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\site-packages\ChimeraX_main.py", line 1015 in 
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\runpy.py", line 87 in _run_code
  File "C:\Program Files\ChimeraX 1.2.1\bin\lib\runpy.py", line 194 in _run_module_as_main


Log:
UCSF ChimeraX version: 1.2.1 (2021-05-05)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\Users\\\Chema\\\tacoxDNA\\\tacoxDNA\\\src\\\f_centroid_161122_7b_01b_mean_1.dat.pdb

Summary of feedback from opening
C:\\\Users\\\Chema\\\tacoxDNA\\\tacoxDNA\\\src\\\f_centroid_161122_7b_01b_mean_1.dat.pdb  
---  
warnings | Ignored bad PDB record found on line 788  
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Duplicate atom serial number found: 1  
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Duplicate atom serial number found: 75935  
Duplicate atom serial number found: 75936  
Duplicate atom serial number found: 75937  
Duplicate atom serial number found: 75938  
Duplicate atom serial number found: 75939  
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Duplicate atom serial number found: 76946  
Duplicate atom serial number found: 76947  
Duplicate atom serial number found: 76948  
Duplicate atom serial number found: 76949  
Duplicate atom serial number found: 76950  
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Duplicate atom serial number found: 77516  
Duplicate atom serial number found: 77517  
Duplicate atom serial number found: 77518  
Duplicate atom serial number found: 77519  
Duplicate atom serial number found: 77520  
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Duplicate atom serial number found: 78966  
Duplicate atom serial number found: 78967  
Duplicate atom serial number found: 78968  
Duplicate atom serial number found: 78969  
Duplicate atom serial number found: 78970  
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Duplicate atom serial number found: 80204  
Duplicate atom serial number found: 80205  
Duplicate atom serial number found: 80206  
Duplicate atom serial number found: 80207  
Duplicate atom serial number found: 80208  
1454 messages similar to the above omitted  
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Duplicate atom serial number found: 81663  
Duplicate atom serial number found: 81664  
Duplicate atom serial number found: 81665  
Duplicate atom serial number found: 81666  
Duplicate atom serial number found: 81667  
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Duplicate atom serial number found: 82432  
Duplicate atom serial number found: 82433  
Duplicate atom serial number found: 82434  
Duplicate atom serial number found: 82435  
Duplicate atom serial number found: 82436  
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Duplicate atom serial number found: 83798  
Duplicate atom serial number found: 83799  
Duplicate atom serial number found: 83800  
Duplicate atom serial number found: 83801  
Duplicate atom serial number found: 83802  
1515 messages similar to the above omitted  
Ignored bad PDB record found on line 385469  
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Duplicate atom serial number found: 85318  
Duplicate atom serial number found: 85319  
Duplicate atom serial number found: 85320  
Duplicate atom serial number found: 85321  
Duplicate atom serial number found: 85322  
821 messages similar to the above omitted  
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Duplicate atom serial number found: 86144  
Duplicate atom serial number found: 86145  
Duplicate atom serial number found: 86146  
Duplicate atom serial number found: 86147  
Duplicate atom serial number found: 86148  
1618 messages similar to the above omitted  
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Duplicate atom serial number found: 87767  
Duplicate atom serial number found: 87768  
Duplicate atom serial number found: 87769  
Duplicate atom serial number found: 87770  
Duplicate atom serial number found: 87771  
563 messages similar to the above omitted  
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Duplicate atom serial number found: 88335  
Duplicate atom serial number found: 88336  
Duplicate atom serial number found: 88337  
Duplicate atom serial number found: 88338  
Duplicate atom serial number found: 88339  
348 messages similar to the above omitted  
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Duplicate atom serial number found: 88688  
Duplicate atom serial number found: 88689  
Duplicate atom serial number found: 88690  
Duplicate atom serial number found: 88691  
Duplicate atom serial number found: 88692  
1432 messages similar to the above omitted  
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Duplicate atom serial number found: 90125  
Duplicate atom serial number found: 90126  
Duplicate atom serial number found: 90127  
Duplicate atom serial number found: 90128  
Duplicate atom serial number found: 90129  
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Duplicate atom serial number found: 90919  
Duplicate atom serial number found: 90920  
Duplicate atom serial number found: 90921  
Duplicate atom serial number found: 90922  
Duplicate atom serial number found: 90923  
1111 messages similar to the above omitted  
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Duplicate atom serial number found: 92035  
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Duplicate atom serial number found: 92037  
Duplicate atom serial number found: 92038  
Duplicate atom serial number found: 92039  
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Duplicate atom serial number found: 93273  
Duplicate atom serial number found: 93274  
Duplicate atom serial number found: 93275  
Duplicate atom serial number found: 93276  
Duplicate atom serial number found: 93277  
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Duplicate atom serial number found: 94511  
Duplicate atom serial number found: 94512  
Duplicate atom serial number found: 94513  
Duplicate atom serial number found: 94514  
Duplicate atom serial number found: 94515  
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Duplicate atom serial number found: 95553  
Duplicate atom serial number found: 95554  
Duplicate atom serial number found: 95555  
Duplicate atom serial number found: 95556  
Duplicate atom serial number found: 95557  
665 messages similar to the above omitted  
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Duplicate atom serial number found: 96223  
Duplicate atom serial number found: 96224  
Duplicate atom serial number found: 96225  
Duplicate atom serial number found: 96226  
Duplicate atom serial number found: 96227  
1105 messages similar to the above omitted  
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Duplicate atom serial number found: 97333  
Duplicate atom serial number found: 97334  
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Duplicate atom serial number found: 97337  
1679 messages similar to the above omitted  
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Duplicate atom serial number found: 99017  
Duplicate atom serial number found: 99018  
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Duplicate atom serial number found: 99020  
Duplicate atom serial number found: 99021  
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Duplicate atom serial number found: 99553  
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Duplicate atom serial number found: 861  
Duplicate atom serial number found: 862  
Duplicate atom serial number found: 863  
Duplicate atom serial number found: 864  
Duplicate atom serial number found: 865  
501 messages similar to the above omitted  
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Duplicate atom serial number found: 1367  
Duplicate atom serial number found: 1368  
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Duplicate atom serial number found: 1371  
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Duplicate atom serial number found: 2950  
Duplicate atom serial number found: 2951  
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Duplicate atom serial number found: 2953  
Duplicate atom serial number found: 2954  
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Duplicate atom serial number found: 4037  
Duplicate atom serial number found: 4038  
Duplicate atom serial number found: 4039  
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Duplicate atom serial number found: 4041  
1015 messages similar to the above omitted  
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Duplicate atom serial number found: 5057  
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Duplicate atom serial number found: 5061  
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Duplicate atom serial number found: 6774  
Duplicate atom serial number found: 6775  
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827 messages similar to the above omitted  
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Duplicate atom serial number found: 7606  
Duplicate atom serial number found: 7607  
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Duplicate atom serial number found: 7609  
Duplicate atom serial number found: 7610  
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Duplicate atom serial number found: 8911  
Duplicate atom serial number found: 8912  
Duplicate atom serial number found: 8913  
Duplicate atom serial number found: 8914  
Duplicate atom serial number found: 8915  
1355 messages similar to the above omitted  
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Duplicate atom serial number found: 10271  
Duplicate atom serial number found: 10272  
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Duplicate atom serial number found: 10275  
1447 messages similar to the above omitted  
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Duplicate atom serial number found: 11723  
Duplicate atom serial number found: 11724  
Duplicate atom serial number found: 11725  
Duplicate atom serial number found: 11726  
Duplicate atom serial number found: 11727  
1234 messages similar to the above omitted  
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Duplicate atom serial number found: 12962  
Duplicate atom serial number found: 12963  
Duplicate atom serial number found: 12964  
Duplicate atom serial number found: 12965  
Duplicate atom serial number found: 12966  
1364 messages similar to the above omitted  
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Duplicate atom serial number found: 14331  
Duplicate atom serial number found: 14332  
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Duplicate atom serial number found: 14335  
799 messages similar to the above omitted  
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Duplicate atom serial number found: 15135  
Duplicate atom serial number found: 15136  
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Duplicate atom serial number found: 15138  
Duplicate atom serial number found: 15139  
1172 messages similar to the above omitted  
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Duplicate atom serial number found: 16312  
Duplicate atom serial number found: 16313  
Duplicate atom serial number found: 16314  
Duplicate atom serial number found: 16315  
Duplicate atom serial number found: 16316  
599 messages similar to the above omitted  
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Duplicate atom serial number found: 16916  
Duplicate atom serial number found: 16917  
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Duplicate atom serial number found: 16919  
Duplicate atom serial number found: 16920  
1113 messages similar to the above omitted  
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Duplicate atom serial number found: 18034  
Duplicate atom serial number found: 18035  
Duplicate atom serial number found: 18036  
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Duplicate atom serial number found: 18038  
634 messages similar to the above omitted  
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Duplicate atom serial number found: 18673  
Duplicate atom serial number found: 18674  
Duplicate atom serial number found: 18675  
Duplicate atom serial number found: 18676  
Duplicate atom serial number found: 18677  
977 messages similar to the above omitted  
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Duplicate atom serial number found: 19655  
Duplicate atom serial number found: 19656  
Duplicate atom serial number found: 19657  
Duplicate atom serial number found: 19658  
Duplicate atom serial number found: 19659  
665 messages similar to the above omitted  
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Duplicate atom serial number found: 20325  
Duplicate atom serial number found: 20326  
Duplicate atom serial number found: 20327  
Duplicate atom serial number found: 20328  
Duplicate atom serial number found: 20329  
1063 messages similar to the above omitted  
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Duplicate atom serial number found: 21393  
Duplicate atom serial number found: 21394  
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Duplicate atom serial number found: 21396  
Duplicate atom serial number found: 21397  
1169 messages similar to the above omitted  
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Duplicate atom serial number found: 22567  
Duplicate atom serial number found: 22568  
Duplicate atom serial number found: 22569  
Duplicate atom serial number found: 22570  
Duplicate atom serial number found: 22571  
693 messages similar to the above omitted  
Ignored bad PDB record found on line 423451  
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Duplicate atom serial number found: 23265  
Duplicate atom serial number found: 23266  
Duplicate atom serial number found: 23267  
Duplicate atom serial number found: 23268  
Duplicate atom serial number found: 23269  
634 messages similar to the above omitted  
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Duplicate atom serial number found: 23904  
Duplicate atom serial number found: 23905  
Duplicate atom serial number found: 23906  
Duplicate atom serial number found: 23907  
Duplicate atom serial number found: 23908  
856 messages similar to the above omitted  
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Duplicate atom serial number found: 24765  
Duplicate atom serial number found: 24766  
Duplicate atom serial number found: 24767  
Duplicate atom serial number found: 24768  
Duplicate atom serial number found: 24769  
1249 messages similar to the above omitted  
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Duplicate atom serial number found: 26019  
Duplicate atom serial number found: 26020  
Duplicate atom serial number found: 26021  
Duplicate atom serial number found: 26022  
Duplicate atom serial number found: 26023  
821 messages similar to the above omitted  
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Duplicate atom serial number found: 26845  
Duplicate atom serial number found: 26846  
Duplicate atom serial number found: 26847  
Duplicate atom serial number found: 26848  
Duplicate atom serial number found: 26849  
657 messages similar to the above omitted  
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Duplicate atom serial number found: 27507  
Duplicate atom serial number found: 27508  
Duplicate atom serial number found: 27509  
Duplicate atom serial number found: 27510  
Duplicate atom serial number found: 27511  
1298 messages similar to the above omitted  
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Duplicate atom serial number found: 28810  
Duplicate atom serial number found: 28811  
Duplicate atom serial number found: 28812  
Duplicate atom serial number found: 28813  
Duplicate atom serial number found: 28814  
951 messages similar to the above omitted  
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Duplicate atom serial number found: 29766  
Duplicate atom serial number found: 29767  
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Duplicate atom serial number found: 29769  
Duplicate atom serial number found: 29770  
663 messages similar to the above omitted  
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Duplicate atom serial number found: 30434  
Duplicate atom serial number found: 30435  
Duplicate atom serial number found: 30436  
Duplicate atom serial number found: 30437  
Duplicate atom serial number found: 30438  
568 messages similar to the above omitted  
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Duplicate atom serial number found: 31007  
Duplicate atom serial number found: 31008  
Duplicate atom serial number found: 31009  
Duplicate atom serial number found: 31010  
Duplicate atom serial number found: 31011  
665 messages similar to the above omitted  
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Duplicate atom serial number found: 31677  
Duplicate atom serial number found: 31678  
Duplicate atom serial number found: 31679  
Duplicate atom serial number found: 31680  
Duplicate atom serial number found: 31681  
663 messages similar to the above omitted  
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Duplicate atom serial number found: 32345  
Duplicate atom serial number found: 32346  
Duplicate atom serial number found: 32347  
Duplicate atom serial number found: 32348  
Duplicate atom serial number found: 32349  
595 messages similar to the above omitted  
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Duplicate atom serial number found: 32945  
Duplicate atom serial number found: 32946  
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Duplicate atom serial number found: 32948  
Duplicate atom serial number found: 32949  
1170 messages similar to the above omitted  
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Duplicate atom serial number found: 34120  
Duplicate atom serial number found: 34121  
Duplicate atom serial number found: 34122  
Duplicate atom serial number found: 34123  
Duplicate atom serial number found: 34124  
1475 messages similar to the above omitted  
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Duplicate atom serial number found: 35600  
Duplicate atom serial number found: 35601  
Duplicate atom serial number found: 35602  
Duplicate atom serial number found: 35603  
Duplicate atom serial number found: 35604  
1234 messages similar to the above omitted  
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Duplicate atom serial number found: 36839  
Duplicate atom serial number found: 36840  
Duplicate atom serial number found: 36841  
Duplicate atom serial number found: 36842  
Duplicate atom serial number found: 36843  
535 messages similar to the above omitted  
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Duplicate atom serial number found: 37379  
Duplicate atom serial number found: 37380  
Duplicate atom serial number found: 37381  
Duplicate atom serial number found: 37382  
Duplicate atom serial number found: 37383  
696 messages similar to the above omitted  
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Duplicate atom serial number found: 38080  
Duplicate atom serial number found: 38081  
Duplicate atom serial number found: 38082  
Duplicate atom serial number found: 38083  
Duplicate atom serial number found: 38084  
1684 messages similar to the above omitted  
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Duplicate atom serial number found: 39769  
Duplicate atom serial number found: 39770  
Duplicate atom serial number found: 39771  
Duplicate atom serial number found: 39772  
Duplicate atom serial number found: 39773  
1236 messages similar to the above omitted  
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Duplicate atom serial number found: 41010  
Duplicate atom serial number found: 41011  
Duplicate atom serial number found: 41012  
Duplicate atom serial number found: 41013  
Duplicate atom serial number found: 41014  
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Duplicate atom serial number found: 42319  
Duplicate atom serial number found: 42320  
Duplicate atom serial number found: 42321  
Duplicate atom serial number found: 42322  
Duplicate atom serial number found: 42323  
861 messages similar to the above omitted  
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Duplicate atom serial number found: 43185  
Duplicate atom serial number found: 43186  
Duplicate atom serial number found: 43187  
Duplicate atom serial number found: 43188  
Duplicate atom serial number found: 43189  
786 messages similar to the above omitted  
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Duplicate atom serial number found: 43976  
Duplicate atom serial number found: 43977  
Duplicate atom serial number found: 43978  
Duplicate atom serial number found: 43979  
Duplicate atom serial number found: 43980  
719 messages similar to the above omitted  
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Duplicate atom serial number found: 44700  
Duplicate atom serial number found: 44701  
Duplicate atom serial number found: 44702  
Duplicate atom serial number found: 44703  
Duplicate atom serial number found: 44704  
1107 messages similar to the above omitted  
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Duplicate atom serial number found: 45812  
Duplicate atom serial number found: 45813  
Duplicate atom serial number found: 45814  
Duplicate atom serial number found: 45815  
Duplicate atom serial number found: 45816  
1236 messages similar to the above omitted  
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Duplicate atom serial number found: 47053  
Duplicate atom serial number found: 47054  
Duplicate atom serial number found: 47055  
Duplicate atom serial number found: 47056  
Duplicate atom serial number found: 47057  
699 messages similar to the above omitted  
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Duplicate atom serial number found: 47757  
Duplicate atom serial number found: 47758  
Duplicate atom serial number found: 47759  
Duplicate atom serial number found: 47760  
Duplicate atom serial number found: 47761  
1010 messages similar to the above omitted  
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Duplicate atom serial number found: 48772  
Duplicate atom serial number found: 48773  
Duplicate atom serial number found: 48774  
Duplicate atom serial number found: 48775  
Duplicate atom serial number found: 48776  
846 messages similar to the above omitted  
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Duplicate atom serial number found: 49623  
Duplicate atom serial number found: 49624  
Duplicate atom serial number found: 49625  
Duplicate atom serial number found: 49626  
Duplicate atom serial number found: 49627  
987 messages similar to the above omitted  
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Duplicate atom serial number found: 50615  
Duplicate atom serial number found: 50616  
Duplicate atom serial number found: 50617  
Duplicate atom serial number found: 50618  
Duplicate atom serial number found: 50619  
862 messages similar to the above omitted  
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Duplicate atom serial number found: 51482  
Duplicate atom serial number found: 51483  
Duplicate atom serial number found: 51484  
Duplicate atom serial number found: 51485  
Duplicate atom serial number found: 51486  
1077 messages similar to the above omitted  
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Duplicate atom serial number found: 52564  
Duplicate atom serial number found: 52565  
Duplicate atom serial number found: 52566  
Duplicate atom serial number found: 52567  
Duplicate atom serial number found: 52568  
1072 messages similar to the above omitted  
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Duplicate atom serial number found: 53641  
Duplicate atom serial number found: 53642  
Duplicate atom serial number found: 53643  
Duplicate atom serial number found: 53644  
Duplicate atom serial number found: 53645  
1584 messages similar to the above omitted  
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Duplicate atom serial number found: 55230  
Duplicate atom serial number found: 55231  
Duplicate atom serial number found: 55232  
Duplicate atom serial number found: 55233  
Duplicate atom serial number found: 55234  
766 messages similar to the above omitted  
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Duplicate atom serial number found: 56001  
Duplicate atom serial number found: 56002  
Duplicate atom serial number found: 56003  
Duplicate atom serial number found: 56004  
Duplicate atom serial number found: 56005  
884 messages similar to the above omitted  
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Duplicate atom serial number found: 56890  
Duplicate atom serial number found: 56891  
Duplicate atom serial number found: 56892  
Duplicate atom serial number found: 56893  
Duplicate atom serial number found: 56894  
348 messages similar to the above omitted  
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Duplicate atom serial number found: 57243  
Duplicate atom serial number found: 57244  
Duplicate atom serial number found: 57245  
Duplicate atom serial number found: 57246  
Duplicate atom serial number found: 57247  
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Duplicate atom serial number found: 58670  
Duplicate atom serial number found: 58671  
Duplicate atom serial number found: 58672  
Duplicate atom serial number found: 58673  
Duplicate atom serial number found: 58674  
375 messages similar to the above omitted  
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Duplicate atom serial number found: 59050  
Duplicate atom serial number found: 59051  
Duplicate atom serial number found: 59052  
Duplicate atom serial number found: 59053  
Duplicate atom serial number found: 59054  
1474 messages similar to the above omitted  
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Chain information for f_centroid_161122_7b_01b_mean_1.dat.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
E | No description available  
F | No description available  
G | No description available  
H | No description available  
I | No description available  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
  




OpenGL version: 3.3.0 NVIDIA 527.56
OpenGL renderer: NVIDIA GeForce RTX 3070 Laptop GPU/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: ASUSTeK COMPUTER INC.
Model: ASUS TUF Gaming A15 FA506QR_FA506QR
OS: Microsoft Windows 11 Pro (Build 22621)
Memory: 16,539,713,536
MaxProcessMemory: 137,438,953,344
CPU: 16 AMD Ryzen 7 5800H with Radeon Graphics         
OSLanguage: es-ES
Locale: ('es_ES', 'cp1252')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
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    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.12.5
    cftime: 1.4.1
    chardet: 3.0.4
    ChimeraX-AddCharge: 1.0
    ChimeraX-AddH: 2.1.6
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.13.3
    ChimeraX-AtomicLibrary: 3.1.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.5.2
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.1
    ChimeraX-Clipper: 0.16.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.2.1
    ChimeraX-CommandLine: 1.1.4
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.2.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.1.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.1
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.2
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.1
    ChimeraX-Help: 1.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.1
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ISOLDE: 1.2.2
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.2
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.0.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.2
    ChimeraX-MDcrds: 2.2
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.3
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.0.1
    ChimeraX-ModelPanel: 1.0.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.1
    ChimeraX-OpenCommand: 1.5
    ChimeraX-PDB: 2.4.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.0.1
    ChimeraX-ReadPbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RMF: 0.10
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.4
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.3
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.3.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.7.3
    ChimeraX-uniprot: 2.1
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.21
    decorator: 5.0.7
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.17
    imagecodecs: 2020.5.30
    imagesize: 1.2.0
    ipykernel: 5.3.4
    ipython: 7.18.1
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.7
    jupyter-core: 4.7.1
    kiwisolver: 1.3.1
    line-profiler: 2.1.2
    lxml: 4.6.2
    lz4: 3.1.0
    MarkupSafe: 1.1.1
    matplotlib: 3.3.2
    MolecularDynamicsViewer: 1.2
    msgpack: 1.0.0
    netCDF4: 1.5.4
    networkx: 2.5
    numexpr: 2.7.3
    numpy: 1.19.2
    numpydoc: 1.1.0
    openvr: 1.14.1501
    packaging: 20.9
    ParmEd: 3.2.0
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.2.0
    pip: 21.0.1
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.18
    psutil: 5.7.2
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.7.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.1
    pytz: 2021.1
    pywin32: 228
    pyzmq: 22.0.3
    qtconsole: 4.7.7
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.5.2
    Send2Trash: 1.5.0
    SEQCROW: 1.5.9
    setuptools: 50.3.2
    sfftk-rw: 0.6.7.dev1
    six: 1.15.0
    snowballstemmer: 2.1.0
    sortedcontainers: 2.2.2
    Sphinx: 3.2.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.9.3
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.0.5
    urllib3: 1.25.11
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.36.0
    wheel-filename: 1.3.0
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Component: Unassigned → Surface
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Crash in ses_surface_geometry

comment:2 by Tom Goddard, 3 years ago

Resolution: → duplicate
Status: assigned → closed

Tried to compute SES surface for 500,000 or more atoms and machine only had 16 Gbytes of memory. Very likely ran out of memory.

Same as #7905.

Would be nice if an out-of-memory situation just gave an out of memory error message without crashing. Happens too seldom to be worth investigating that fix right now. Crash is in C++ called by ctypes. Probably C++ raises a MemoryError but it doesn't propagate through ctypes.

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