Opened 3 years ago

Closed 3 years ago

#7360 closed defect (can't reproduce)

Crash in atom-spec parser

Reported by: samrmay@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Command Line 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-5.15.0-43-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.4 (2022-06-03 23:39:42 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 0x00007f8ae62beb80 (most recent call first):
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/ast.py", line 99 in __getitem__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/ast.py", line 52 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/ast.py", line 90 in 
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/ast.py", line 60 in upairs
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/ast.py", line 67 in update
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/ast.py", line 19 in __init__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/ast.py", line 90 in copy
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 642 in _try
  File "/usr/lib/ucsf-chimerax/lib/python3.9/contextlib.py", line 119 in __enter__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 679 in _choice
  File "/usr/lib/ucsf-chimerax/lib/python3.9/contextlib.py", line 119 in __enter__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 688 in _optional
  File "/usr/lib/ucsf-chimerax/lib/python3.9/contextlib.py", line 119 in __enter__
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 132 in _as_term_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/_atomspec.py", line 89 in _atom_specifier_
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 497 in _invoke_rule
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 458 in _call
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 59 in wrapper
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/grako/contexts.py", line 206 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 181 in _parse_unquoted
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 110 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1297 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 980 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 1070 in evaluate
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/cli.py", line 1298 in parse
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/basic_actions/cmd.py", line 31 in selector
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 920 in find_matches
  File "/usr/lib/ucsf-chimerax/lib/python3.9/site-packages/chimerax/core/commands/atomspec.py", line 983 in find_matches
  ...
===== Log before crash start =====
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/ct-state/series-4A-2/series-4A-2.out.plots/detach_a.9.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/ct-
> state/series-4A-2/series-4A-2.out.plots/detach_a.8.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/ct-
> state/series-4A-2/series-4A-2.out.plots/detach_a.7.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/ct-
> state/series-4A-2/series-4A-2.out.plots/detach_a.6.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/ct-
> state/series-4A-2/series-4A-2.out.plots/detach_a.5.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/ct-
> state/series-4A-2/series-4A-2.out.plots/detach_a.4.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/ct-
> state/series-4A-2/series-4A-2.out.plots/detach_a.3.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/ct-
> state/series-4A-2/series-4A-2.out.plots/detach_a.39.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/ct-
> state/series-4A-2/series-4A-2.out.plots/detach_a.38.cube

Opened detach_a.9.cube as #1.1, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.00133,0.00133, step 1, values float32  
Opened detach_a.8.cube as #1.2, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.00153,0.00153, step 1, values float32  
Opened detach_a.7.cube as #1.3, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.00109,0.00109, step 1, values float32  
Opened detach_a.6.cube as #1.4, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.00155,0.00155, step 1, values float32  
Opened detach_a.5.cube as #1.5, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.0016,0.0016, step 1, values float32  
Opened detach_a.4.cube as #1.6, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.0015,0.0015, step 1, values float32  
Opened detach_a.3.cube as #1.7, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.00113,0.00113, step 1, values float32  
Opened detach_a.39.cube as #1.8, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.00111,0.00111, step 1, values float32  
Opened detach_a.38.cube as #1.9, grid size 72,51,27, pixel 0.299,0.303,0.301,
shown at level -0.00147,0.00147, step 1, values float32  

> close

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.0.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/py-
> dma-full-hyperfine-series/series-1A/series-1A.out.plots/detach_a.0.cube

Opened attach_a.0.cube as #1.1, grid size 62,51,27, pixel 0.3,0.303,0.303,
shown at level -0.211,0.211, step 1, values float32  
Opened detach_a.0.cube as #1.2, grid size 62,51,27, pixel 0.3,0.303,0.303,
shown at level -0.00142,0.00142, step 1, values float32  

> hide #!1.1 models

> show #!1.1 models

> hide #!1.2 models

> close #1

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.0.cube
> /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-dma/py-
> dma-full-hyperfine-series/series-1A/series-1A.out.plots/detach_a.0.cube

Opened attach_a.0.cube as #1.1, grid size 62,51,27, pixel 0.3,0.303,0.303,
shown at level -0.211,0.211, step 1, values float32  
Opened detach_a.0.cube as #1.2, grid size 62,51,27, pixel 0.3,0.303,0.303,
shown at level -0.00142,0.00142, step 1, values float32  

> color attach_a.0.cube red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach_a.0.cube medium blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> name tm1 #1.1

> color tm1 red

> hide #!1.2 models

> show #!1.2 models

> hide #!1.2 models

> volume #1.1 level -0.2114 level 3.115

> volume #1.1 level 1.616e-09 level 3.115

> volume #1.1 level 1.616e-09 level 0.1605

> show #!1.2 models

> hide #!1.2 models

> hide #!1.1 models

> show #!1.2 models

> color detach_a.0.cube red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color detach_a.0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color detach_a red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.0.cube name attach0

Opened attach0 as #2, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.211,0.211, step 1, values float32  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.0.cube name detach0

Opened detach0 as #3, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00142,0.00142, step 1, values float32  

> close

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.0.cube name detach0

Opened detach0 as #1, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00142,0.00142, step 1, values float32  

> hide #!1 models

> show #!1 models

> hide #1.1 models

> show #1.1 models

> hide #1.2 models

> show #1.2 models

> close

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.0.cube name attach0

Opened attach0 as #1, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.211,0.211, step 1, values float32  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.0.cube name detach0

Opened detach0 as #2, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00142,0.00142, step 1, values float32  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> combine attach0 detach0

Expected a keyword  

> combine

No structures specified  

> combine attach0

Expected a keyword  

> combine #1-2

No structures specified  

> combine #1

No structures specified  

> close

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.0.cube name attach0

Opened attach0 as #1, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.211,0.211, step 1, values float32  

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.0.cube name detach0

Opened detach0 as #2, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00142,0.00142, step 1, values float32  

> color detach0 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.1.cube name attach1

Opened attach1 as #3, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00163,0.00163, step 1, values float32  

> color attach1 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.1.cube name detach1

Opened detach1 as #4, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00169,0.00169, step 1, values float32  

> color detach1 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach1

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

> hide detach1

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.10.cube name attach10

Opened attach10 as #5, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00164,0.00164, step 1, values float32  

> color attach10 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.10.cube name detach10

Opened detach10 as #6, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.0018,0.0018, step 1, values float32  

> color detach10 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach10

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

> hide detach10

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.11.cube name attach11

Opened attach11 as #7, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00147,0.00147, step 1, values float32  

> color attach11 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.11.cube name detach11

Opened detach11 as #8, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.0016,0.0016, step 1, values float32  

> color detach11 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach11

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

> hide detach11

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.12.cube name attach12

Opened attach12 as #9, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00151,0.00151, step 1, values float32  

> color attach12 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.12.cube name detach12

Opened detach12 as #10, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00166,0.00166, step 1, values float32  

> color detach12 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach12

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

> hide detach12

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.13.cube name attach13

Opened attach13 as #11, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00154,0.00154, step 1, values float32  

> color attach13 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.13.cube name detach13

Opened detach13 as #12, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00172,0.00172, step 1, values float32  

> color detach13 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach13

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

> hide detach13

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.14.cube name attach14

Opened attach14 as #13, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00123,0.00123, step 1, values float32  

> color attach14 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.14.cube name detach14

Opened detach14 as #14, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00178,0.00178, step 1, values float32  

> color detach14 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach14

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

> hide detach14

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.15.cube name attach15

Opened attach15 as #15, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.000338,0.000338, step 1, values float32  

> color attach15 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.15.cube name detach15

Opened detach15 as #16, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00168,0.00168, step 1, values float32  

> color detach15 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach15

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

> hide detach15

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.16.cube name attach16

Opened attach16 as #17, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.000296,0.000296, step 1, values float32  

> color attach16 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.16.cube name detach16

Opened detach16 as #18, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.0017,0.0017, step 1, values float32  

> color detach16 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach16

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

> hide detach16

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.17.cube name attach17

Opened attach17 as #19, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.000528,0.000528, step 1, values float32  

> color attach17 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.17.cube name detach17

Opened detach17 as #20, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.0013,0.0013, step 1, values float32  

> color detach17 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach17

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

> hide detach17

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.18.cube name attach18

Opened attach18 as #21, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00105,0.00105, step 1, values float32  

> color attach18 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.18.cube name detach18

Opened detach18 as #22, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00154,0.00154, step 1, values float32  

> color detach18 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach18

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

> hide detach18

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.19.cube name attach19

Opened attach19 as #23, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.000424,0.000424, step 1, values float32  

> color attach19 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.19.cube name detach19

Opened detach19 as #24, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00131,0.00131, step 1, values float32  

> color detach19 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach19

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

> hide detach19

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.2.cube name attach2

Opened attach2 as #25, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.0014,0.0014, step 1, values float32  

> color attach2 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.2.cube name detach2

Opened detach2 as #26, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.0016,0.0016, step 1, values float32  

> color detach2 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach2

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

> hide detach2

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.3.cube name attach3

Opened attach3 as #27, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00124,0.00124, step 1, values float32  

> color attach3 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.3.cube name detach3

Opened detach3 as #28, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00129,0.00129, step 1, values float32  

> color detach3 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach3

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

> hide detach3

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.4.cube name attach4

Opened attach4 as #29, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00153,0.00153, step 1, values float32  

> color attach4 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.4.cube name detach4

Opened detach4 as #30, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00168,0.00168, step 1, values float32  

> color detach4 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach4

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

> hide detach4

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.5.cube name attach5

Opened attach5 as #31, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00162,0.00162, step 1, values float32  

> color attach5 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.5.cube name detach5

Opened detach5 as #32, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00179,0.00179, step 1, values float32  

> color detach5 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach5

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

> hide detach5

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.6.cube name attach6

Opened attach6 as #33, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00161,0.00161, step 1, values float32  

> color attach6 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.6.cube name detach6

Opened detach6 as #34, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00171,0.00171, step 1, values float32  

> color detach6 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach6

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

> hide detach6

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.7.cube name attach7

Opened attach7 as #35, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00127,0.00127, step 1, values float32  

> color attach7 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.7.cube name detach7

Opened detach7 as #36, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00139,0.00139, step 1, values float32  

> color detach7 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach7

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

> hide detach7

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.8.cube name attach8

Opened attach8 as #37, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00167,0.00167, step 1, values float32  

> color attach8 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.8.cube name detach8

Opened detach8 as #38, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00174,0.00174, step 1, values float32  

> color detach8 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach8

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

> hide detach8

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

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.9.cube name attach9

Opened attach9 as #39, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00165,0.00165, step 1, values float32  

> color attach9 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/detach_a.9.cube name detach9

Opened detach9 as #40, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.00174,0.00174, step 1, values float32  

> color detach9 blue

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> hide attach9

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

> hide detach9

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

> hide #!40 models

> hide #!39 models

> hide #!38 models

> hide #!37 models

> hide #!36 models

> hide #!35 models

> hide #!34 models

> hide #!33 models

> hide #!32 models

> hide #!31 models

> hide #!30 models

> hide #!29 models

> hide #!28 models

> hide #!27 models

> hide #!26 models

> hide #!25 models

> hide #!24 models

> hide #!23 models

> hide #!22 models

> hide #!21 models

> hide #!20 models

> hide #!19 models

> hide #!18 models

> hide #!17 models

> hide #!16 models

> hide #!15 models

> hide #!14 models

> hide #!13 models

> hide #!12 models

> hide #!11 models

> hide #!10 models

> hide #!9 models

> hide #!7 models

> hide #!8 models

> hide #!6 models

> hide #!5 models

> hide #!4 models

> hide #!3 models

> hide #!2 models

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 models 0

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 models red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 models red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 models red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 models red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 models red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 models red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color #1 red

> color #1.1 red

> color #1.1 blue

> color #1.2 blue

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0.1 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color attach0 random red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> name #1 tm1

Not registering illegal selector name "#1"  

> name tm1 #1

> color tm1 red

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> color red

> color attach0

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> name delete

Missing or invalid "name" argument: Expected a text string  

> name delete all

> hide #!7 target m

> show #!7 target m

> close #7

> close

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.0.cube name attach0

Opened attach0 as #1, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.211,0.211, step 1, values float32  

> color attach0 red

Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword  

> name attach0 #1

> color attach0 red

> close

> open /home/samrmay/Documents/subotnik-summer-project-2022/qchem-jobs/py-
> dma/py-dma-full-hyperfine-
> series/series-1A/series-1A.out.plots/attach_a.0.cube name attach0

Opened attach0 as #1, grid size 62,51,27, pixel 0.3,0.303,0.303, shown at
level -0.211,0.211, step 1, values float32  

> name attach0 attach0


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

Log:
UCSF ChimeraX version: 1.4 (2022-06-03)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  




OpenGL version: 4.6 (Core Profile) Mesa 22.0.1
OpenGL renderer: Mesa Intel(R) Xe Graphics (TGL GT2)
OpenGL vendor: Intel

Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: xcb

XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu-xorg
XDG_SESSION_DESKTOP=ubuntu-xorg
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:0
Manufacturer: Framework
Model: Laptop
OS: Ubuntu 22.04 jammy
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:            15Gi       5.1Gi       2.5Gi       1.8Gi       7.9Gi       8.2Gi
	Swap:          2.0Gi          0B       2.0Gi

Graphics:
	00:02.0 VGA compatible controller [0300]: Intel Corporation TigerLake-LP GT2 [Iris Xe Graphics] [8086:9a49] (rev 01)	
	Subsystem: Device [f111:0001]	
	Kernel driver in use: i915

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.10.1
    backcall: 0.2.0
    blockdiag: 3.0.0
    certifi: 2022.5.18.1
    cftime: 1.6.0
    charset-normalizer: 2.0.12
    ChimeraX-AddCharge: 1.2.3
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.4.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.2
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.39.1
    ChimeraX-AtomicLibrary: 7.0
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.1
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.7
    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: 2.2.4
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.1
    ChimeraX-CommandLine: 1.2.3
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.4
    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: 1.1
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.2
    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: 1.1.1
    ChimeraX-LinuxSupport: 1.0
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    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: 2.0.6
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.7
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.5.5
    ChimeraX-ModelPanel: 1.3.2
    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: 1.9
    ChimeraX-PDB: 2.6.6
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    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: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.6
    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: 1.8
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.0.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.1
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.18.3
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.1.2
    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: 1.1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.26
    debugpy: 1.6.0
    decorator: 5.1.1
    distro: 1.6.0
    docutils: 0.17.1
    entrypoints: 0.4
    filelock: 3.4.2
    fonttools: 4.33.3
    funcparserlib: 1.0.0
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.27
    imagecodecs: 2021.11.20
    imagesize: 1.3.0
    ipykernel: 6.6.1
    ipython: 7.31.1
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.0.3
    jupyter-client: 7.1.0
    jupyter-core: 4.10.0
    kiwisolver: 1.4.2
    line-profiler: 3.4.0
    lxml: 4.7.1
    lz4: 3.1.10
    MarkupSafe: 2.1.1
    matplotlib: 3.5.1
    matplotlib-inline: 0.1.3
    msgpack: 1.0.3
    nest-asyncio: 1.5.5
    netCDF4: 1.5.8
    networkx: 2.6.3
    numexpr: 2.8.1
    numpy: 1.22.1
    openvr: 1.16.802
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.0.1
    pip: 21.3.1
    pkginfo: 1.8.2
    prompt-toolkit: 3.0.29
    psutil: 5.9.0
    ptyprocess: 0.7.0
    pycollada: 0.7.2
    pydicom: 2.2.2
    Pygments: 2.11.2
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.0
    PyQt6-Qt6: 6.3.0
    PyQt6-sip: 13.3.1
    PyQt6-WebEngine-commercial: 6.3.0
    PyQt6-WebEngine-Qt6: 6.3.0
    python-dateutil: 2.8.2
    pytz: 2022.1
    pyzmq: 23.1.0
    qtconsole: 5.3.0
    QtPy: 2.1.0
    RandomWords: 0.3.0
    requests: 2.27.1
    scipy: 1.7.3
    Send2Trash: 1.8.0
    SEQCROW: 1.4.4
    setuptools: 59.8.0
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.3.2
    sphinx-autodoc-typehints: 1.15.2
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    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-community: 1.0.0
    tables: 3.7.0
    tifffile: 2021.11.2
    tinyarray: 1.2.4
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.9
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.1
    wheel-filename: 1.3.0

Change History (4)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Command Line
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Crash in atom-spec parser

comment:2 by Eric Pettersen, 3 years ago

Status: accepted → feedback

Hi Sam,

Thanks for reporting this problem. Do you remember the command you were using when this crash occurred?

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

in reply to:  3 ; comment:3 by samrmay@…, 3 years ago 

Hi Eric,

Sorry for the late reply. I was using the name command on a .cube file with
multiple surfaces. I have tried replicating the issue using the same files
and commands with no success. Sorry I could not be of more help, but let me
know if I can provide any other information.

Best,

Sam

On Mon, Aug 1, 2022 at 1:25 PM ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu>
wrote:

comment:4 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: feedback → closed

We intend to change our command parser anyway, which will probably solve this problem as a side effect, so no worries!

--Eric

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