Crash in event loop after session opened

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.13.0-44-generic-x86_64-with-glibc2.31
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
Last time you used ChimeraX it crashed.
Please describe steps that led to the crash here.
Fatal Python error: Segmentation fault

Thread 0x00007f3235908700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 316 in wait
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 574 in wait
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 1284 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f318f7fe700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 576 in _handle_results
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f318ffff700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 528 in _handle_tasks
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31acff9700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/selectors.py", line 416 in select
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/connection.py", line 936 in wait
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 499 in _wait_for_updates
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 519 in _handle_workers
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31ad7fa700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31adffb700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31ae7fc700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31aeffd700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31af7fe700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31affff700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31ccff9700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31cd7fa700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31cdffb700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31ce7fc700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31ceffd700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31cf7fe700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31cffff700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31f0ff9700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31f17fa700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31f1ffb700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31f27fc700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31f2ffd700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31f37fe700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Thread 0x00007f31f3fff700 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/multiprocessing/pool.py", line 114 in worker
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 910 in run
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 973 in _bootstrap_inner
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/threading.py", line 930 in _bootstrap

Current thread 0x00007f32bb657740 (most recent call first):
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/site-packages/chimerax/ui/gui.py", line 301 in event_loop
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 867 in init
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/site-packages/ChimeraX_main.py", line 1018 in 
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/runpy.py", line 87 in _run_code
  File "/cs/group/grp-cryoem/apps/chimerax_1.3ubuntu20.04_amd64/ucsf-chimerax/lib/python3.9/runpy.py", line 197 in _run_module_as_main
===== Log before crash start =====
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/ad/lxhome/k/kedarias/Linux/UVG-spike/figures/7puy.pdb

7puy.pdb title:  
Structure of the membrane soluble spike complex from the lassa virus In A
C3-symmetric map [more info...]  
  
Chain information for 7puy.pdb #1  
---  
Chain | Description | UniProt  
A B C | PRE-GP-C | GLYC_LASSJ  
a b c | GP2 | GLYC_LASSJ  
  
Non-standard residues in 7puy.pdb #1  
---  
BDP — β-D-glucopyranuronic acid (β-D-glucuronic acid; D-glucuronic acid;
glucuronicacid)  
NAG — 2-acetamido-2-deoxy-β-D-glucopyranose (N-acetyl-β-D-glucosamine;
2-acetamido-2-deoxy-β-D-glucose; 2-acetamido-2-deoxy-D-glucose;
2-acetamido-2-deoxy-glucose; N-acetyl-D-glucosamine)  
XYS — α-D-xylopyranose (α-D-xylose; D-xylose; xylose; xylopyranose)  
  

> set bgColor white

> lighting soft

> hide atoms

> show cartoons

> display #.NAG

> show #.NAG

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> display #:NAG

> show #:NAG

Expected a collection of one of 'atoms', 'bonds', 'cartoons', 'models',
'pbonds', 'pseudobonds', 'ribbons', or 'surfaces' or a keyword  

> display :NAG

> color bychain

> color salmon :NAG

Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword  

> color :NAG salmon

> show surfaces

> color :NAG grey

> color #1:1-100 magenta

> color #1:101-400 teal

> color #1:101-500 teal

> save /home/ad/lxhome/k/kedarias/Linux/UVG-spike/figures/test-session-with-
> mammalian-arenavirus-spike.cxs

> color #1/A:101-500 dimgrey

> color #1/A:1-100 light grey

> color bychain

> hide surfaces

> graphics silhouettes true

> select clear

> ui tool show "Side View"

> color #1:1-100 magenta

> color #1:101-500 teal

> open /home/ad/lxhome/k/kedarias/Linux/UVG-spike/figures/emd_13662.map

Opened emd_13662.map as #2, grid size 256,256,256, pixel 1.04, shown at level
0.0454, step 1, values float32  

> volume #2 level 0.1936

> hide #!2 models

> open /home/ad/lxhome/k/kedarias/Linux/UVG-spike/figures/emd_8630.map

Opened emd_8630.map as #3, grid size 150,150,150, pixel 2.15, shown at level
0.00479, step 1, values float32  

> hide #!1 models

> volume #3 level 0.003128

> ui tool show "Hide Dust"

> surface dust #3 size 12.9

> surface dust #3 size 3.9

> surface dust #3 size 30.9

> surface dust #3 size 40.9

> color #1:101-500 teal

> surface dust #3 size 4.9

> surface dust #3 size 45.9

> color #1:101-500 teal

> volume #3 level 0.002488

> volume #3 level 0.003128

> ui tool show "Surface Color"

> color radial #3.1 palette #ff0000:#ffffff:#0000ff

> color radial #3.1 palette 191,#ff0000:319.2,#ffffff:447.4,#0000ff center
> 160.67,159.46,177.11

> color radial #3.1 palette 191,#ff0000:319.2,#ffffff:447.4,#0000ff center
> 160.67,159.46,200.11

> color radial #3.1 palette 191,#ff0000:319.2,#ffffff:447.4,#0000ff center
> 16.67,159.46,200.11

> color height #3.1 palette 191,#ff0000:319.2,#ffffff:447.4,#0000ff center
> 16.67,159.46,200.11

> color radial #3.1 palette 191,#ff0000:319.2,#ffffff:447.4,#0000ff center
> 16.67,159.46,200.11

> color radial #3.1 palette 191,#fcaf3e:319.2,#fce94f:447.4,#8ae234 center
> 3,50,100

> color radial #3.1 palette 191,#fcaf3e:319.2,#fce94f:447.4,#8ae234 center
> 3,50,70

> color radial #3.1 palette 160,#fcaf3e:190,#fce94f:200,#8ae234 center
> 160.67,159.46,177.11

> color radial #3.1 palette 100,#fcaf3e:150,#fce94f:190,#8ae234 center
> 160.67,159.46,177.11

> color radial #3.1 palette 100,#00ffff:150,#fce94f:190,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 150,#00ffff:120,#fce94f:100,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 150,#00ffff:140,#fce94f:100,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 150,#00ffff:100,#fce94f:90,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 150,#00ffff:90,#fce94f:60,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 140,#00ffff:90,#fce94f:60,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 100,#00ffff:90,#fce94f:60,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 110,#00ffff:90,#fce94f:60,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 130,#00ffff:110,#fce94f:60,#fcaf3e center
> 160.67,159.46,177.11

> color radial #3.1 palette 130,#00ffff:100,#fce94f:60,#fcaf3e center
> 160.67,159.46,177.11

> ui tool show "Hide Dust"

> surface undust #3

> ui tool show "Segment Map"

Select a density map in the Segment map field  
Segmenting emd_8630.map, density threshold 0.003128  
Only showing 60 of 76 regions.  
Showing 60 of 76 region surfaces  
500 watershed regions, grouped to 76 regions  
Showing emd_8630.seg - 76 regions, 60 surfaces  

> hide #!4 models

> show #!4 models

> hide #!4 models

> close #4

Segmenting emd_8630.map, density threshold 0.003128  
Only showing 60 of 447 regions.  
Showing 60 of 447 region surfaces  
Only showing 60 of 61 regions.  
Showing 60 of 61 region surfaces  
447 watershed regions, grouped to 61 regions  
Showing emd_8630.seg - 61 regions, 60 surfaces  

> close #4

Segmenting emd_8630.map, density threshold 0.003128  
Only showing 60 of 283 regions.  
Showing 60 of 283 region surfaces  
Showing 54 region surfaces  
283 watershed regions, grouped to 54 regions  
Showing emd_8630.seg - 54 regions, 54 surfaces  

> close #4

Segmenting emd_8630.map, density threshold 0.003128  
Only showing 3 of 283 regions.  
Showing 3 of 283 region surfaces  
Only showing 3 of 54 regions.  
Showing 3 of 54 region surfaces  
283 watershed regions, grouped to 54 regions  
Showing emd_8630.seg - 54 regions, 3 surfaces  

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

> hide #!3 models

> show #!3 models

Segmenting emd_8630.map, density threshold 0.003128  
Only showing 10 of 283 regions.  
Showing 10 of 283 region surfaces  
Only showing 10 of 54 regions.  
Showing 10 of 54 region surfaces  
283 watershed regions, grouped to 54 regions  
Showing emd_8630.seg - 54 regions, 10 surfaces  
Grouped 6 regions  

> select clear

> close #4

> surface dust #3 size 42.73

> surface dust #3 size 4.73

> surface dust #3 size 45.73

> color #1:101-500 teal

> color radial #3.1 palette 130,#00ffff:100,#fce94f:60,#fcaf3e

> color radial #3.1 palette 13,#00ffff:10,#fce94f:60,#fcaf3e

> color radial #3.1 palette 40,#00ffff:50,#fce94f:60,#fcaf3e

> color radial #3.1 palette 60,#00ffff:100,#fce94f:150,#fcaf3e

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e center 0,0,40

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e center 0,0,100

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e center 0,40,0

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e center 40,40,0

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e center 40,10,0

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e center
> 110,10,0

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e center
> 160,40,0

> color radial #3.1 palette 150,#00ffff:300,#fce94f:600,#fcaf3e center
> 160,60,0

> color radial #3.1 palette 600,#00ffff:300,#fce94f:150,#fcaf3e center
> 160,60,0

> color radial #3.1 palette 300,#00ffff:200,#fce94f:150,#fcaf3e center
> 160,60,0

> color radial #3.1 palette 300,#00ffff:250,#fce94f:100,#fcaf3e center
> 160,60,0

> color radial #3.1 palette 300,#00ffff:230,#fce94f:120,#fcaf3e center
> 160,60,0

> color radial #3.1 palette 300,#00ffff:220,#fce94f:120,#fcaf3e center
> 160,60,0

> save /home/ad/lxhome/k/kedarias/Linux/UVG-spike/figures/test-session-with-
> mammalian-ebolavirus-spike.cxs

> color radial #3.1 palette 300,#00ffff:220,#fce94f:120,#fcaf3e center
> 160,60,-10

> color radial #3.1 palette 300,#00ffff:220,#fce94f:120,#fcaf3e center
> 160,60,-20

> color radial #3.1 palette 300,#00ffff:220,#fce94f:120,#fcaf3e center
> 160,60,-30

> color radial #3.1 palette 300,#00ffff:220,#fce94f:120,#fcaf3e center
> 160,70,-30

> color radial #3.1 palette 300,#00ffff:220,#fce94f:120,#fcaf3e center
> 160,100,-30

> color radial #3.1 palette 300,#00ffff:220,#fce94f:120,#fcaf3e center
> 160,150,-30

> color radial #3.1 palette 300,#00ffff:220,#fce94f:120,#fcaf3e center
> 160,150,-50

> color radial #3.1 palette 300,#00ffff:230,#fce94f:120,#fcaf3e center
> 160,150,-50

> color radial #3.1 palette 300,#00ffff:250,#fce94f:120,#fcaf3e center
> 160,150,-50

> color radial #3.1 palette 280,#00ffff:250,#fce94f:120,#fcaf3e center
> 160,150,-50

> save /home/ad/lxhome/k/kedarias/Linux/UVG-spike/figures/test-session-with-
> mammalian-ebolavirus-spike.cxs

> lighting soft

> open /home/ad/lxhome/k/kedarias/Linux/UVG-spike/figures/test-session-with-
> mammalian-arenavirus-spike.cxs

opened ChimeraX session  


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

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.3 (Core Profile) Mesa 21.2.6
OpenGL renderer: NV137
OpenGL vendor: nouveau
Manufacturer: LENOVO
Model: 30DH00HJMT
OS: Ubuntu 20.04 focal
Architecture: 64bit ELF
Virutal Machine: none
CPU: 20 Intel(R) Core(TM) i9-10900K CPU @ 3.70GHz
Cache Size: 20480 KB
Memory:
	              total        used        free      shared  buff/cache   available
	Mem:           15Gi       9.8Gi       1.0Gi       143Mi       4.5Gi       5.1Gi
	Swap:          15Gi       1.0Mi        15Gi

Graphics:
	01:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP107 [GeForce GTX 1050 Ti] [10de:1c82] (rev a1)	
	Subsystem: Micro-Star International Co., Ltd. [MSI] GP107 [GeForce GTX 1050 Ti] [1462:8c96]	
	Kernel driver in use: nouveau
Locale: ('en_GB', 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.10.8
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    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: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    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: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    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: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 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: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    distro: 1.6.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    line-profiler: 3.3.0
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.3
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0