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Opened 4 hours ago
#19462 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Linux-6.14.0-36-generic-x86_64-with-glibc2.39
ChimeraX Version: 1.11rc202511260300 (2025-11-26 03:00:12 UTC)
Description
I tried to save session after deleting unwanted cavities found by Find Cavities tool.
Log:
Startup Messages
---
note | /home/maciek/.local/share/ChimeraX/1.11/lib/python3.11/site-packages/chimerax/clipper/__init__.py:29: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
import pkg_resources
UCSF ChimeraX version: 1.11rc202511260300 (2025-11-26)
© 2016-2025 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/maciek/Pulpit/Validation_AOD/AOD_BocOrn/7_aod_bocorn_xyzout_coot_rebuild_1-coot-4.pdb
Chain information for 7_aod_bocorn_xyzout_coot_rebuild_1-coot-4.pdb #1
---
Chain | Description
A | No description available
B | No description available
108 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
6734 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> find cavities
Unknown command: find cavities
> Find Cavities
Unknown command: Find Cavities
> ui tool show "Find Cavities"
pyKVFinder module not installed; fetching from PyPi repository...
Errors may have occurred when running pip:
pip standard error:
\---
ERROR: pip's dependency resolver does not currently take into account all the
packages that are installed. This behaviour is the source of the following
dependency conflicts.
scipy 1.14.0 requires numpy<2.3,>=1.23.5, but you have numpy 2.3.5 which is
incompatible.
nptyping 2.5.0 requires numpy<2.0.0,>=1.20.0; python_version >= "3.8", but you
have numpy 2.3.5 which is incompatible.
\---
pip standard output:
\---
\---
pyKVFinder module installed from PyPi repository.
> kvfinder
47 cavities found for 7_aod_bocorn_xyzout_coot_rebuild_1-coot-4.pdb #1
7_aod_bocorn_xyzout_coot_rebuild_1-coot-4.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
1.2.8 | | 1470.53 | 1092.86 | 6808 | 14.05 | 3.56
1.2.25 | | 948.67 | 813.34 | 4392 | 6.81 | 1.69
1.2.16 | | 92.02 | 121.85 | 426 | 0 | 0
1.2.24 | | 86.83 | 110.95 | 402 | 0 | 0
1.2.30 | | 83.81 | 116.31 | 388 | 0 | 0
1.2.46 | | 51.84 | 51.04 | 240 | 2.81 | 0.93
1.2.26 | | 49.25 | 56.74 | 228 | 3.5 | 1.22
1.2.22 | | 38.45 | 49.67 | 178 | 3 | 1.19
1.2.14 | | 32.62 | 42.67 | 151 | 3 | 1.14
1.2.20 | | 27.86 | 36.52 | 129 | 2.4 | 0.67
1.2.3 | | 27.65 | 33.32 | 128 | 2.24 | 0.7
1.2.5 | | 27.65 | 49.13 | 128 | 0 | 0
1.2.29 | | 27 | 44.51 | 125 | 0 | 0
1.2.4 | | 25.92 | 44.39 | 120 | 0 | 0
1.2.32 | | 25.27 | 43.38 | 117 | 0 | 0
1.2.38 | | 24.19 | 33.86 | 112 | 1.9 | 0.64
1.2.27 | | 23.98 | 33.2 | 111 | 2.4 | 0.74
1.2.23 | | 22.9 | 41.28 | 106 | 0 | 0
1.2.45 | | 22.46 | 35.7 | 104 | 0 | 0
1.2.35 | | 21.38 | 37.45 | 99 | 0 | 0
1.2.17 | | 21.17 | 39.07 | 98 | 0 | 0
1.2.36 | | 20.74 | 41.19 | 96 | 0 | 0
1.2.31 | | 20.3 | 30.77 | 94 | 1.2 | 0.38
1.2.28 | | 19.87 | 36.19 | 92 | 0 | 0
1.2.34 | | 19.87 | 36.19 | 92 | 0 | 0
1.2.44 | | 19.87 | 36.19 | 92 | 0 | 0
1.2.39 | | 17.28 | 36.68 | 80 | 0 | 0
1.2.9 | | 16.85 | 32.3 | 78 | 0 | 0
1.2.40 | | 16.85 | 32.3 | 78 | 0 | 0
1.2.41 | | 16.85 | 32.3 | 78 | 0 | 0
1.2.6 | | 14.9 | 23.19 | 69 | 1.2 | 0.39
1.2.18 | | 12.96 | 21.12 | 60 | 1.2 | 0.42
1.2.7 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.11 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.12 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.21 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.37 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.42 | | 12.31 | 29.54 | 57 | 0 | 0
1.2.10 | | 11.66 | 19.69 | 54 | 1.2 | 0.27
1.2.33 | | 11.23 | 19.29 | 52 | 1.34 | 0.48
1.2.43 | | 10.15 | 18.9 | 47 | 1.2 | 0.36
1.2.13 | | 9.94 | 17.83 | 46 | 1.34 | 0.38
1.2.15 | | 9.72 | 18.72 | 45 | 0.85 | 0.27
1.2.47 | | 9.72 | 19.4 | 45 | 1.34 | 0.47
1.2.2 | | 9.07 | 15.34 | 42 | 0.6 | 0.21
1.2.19 | | 8.86 | 17.53 | 41 | 0.85 | 0.24
1.2.1 | | 7.13 | 14.82 | 33 | 1.2 | 0.35
> view #1.2.8 @< 3.5
> zoom 0.75
moved plane near -45.40525271862024 [ 0.02935512 -0.99228482 -0.1204538 ]
moved plane far -45.40525271862024 [ 0.02935512 -0.99228482 -0.1204538 ]
> surface #1.2.1-47 transparency 50
> ~surface #1.2
> surface #1.2.8
> show
> #!1/A:221-225,227,277-288/B:36-38,101,104-108,111-112,129,133,164-178,196,198-200,208,211,213,273-274,296,349-352,383,385-389,408,411-414
> view #!1.2.25 @< 3.5
> zoom 0.75
moved plane near -46.79161221010951 [-0.9659348 -0.08433793 0.24465706]
moved plane far -46.79161221010951 [-0.9659348 -0.08433793 0.24465706]
> ~surface #1.2
> surface #!1.2.25
> show
> #!1/A:101,105-108,111-112,129,133,165-178,198-201,205,208,211,213,273,296,349-353,381,383-389,391-392,408-414/B:222-225,227,277-281,283-288
> open /home/maciek/Pulpit/Validation_AOD/AOD_TRS/AOD_TRS_refmac43-coot-2.pdb
Chain information for AOD_TRS_refmac43-coot-2.pdb #2
---
Chain | Description
A | No description available
B | No description available
73 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
6822 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> open
> /home/maciek/Pulpit/Validation_AOD/AOD_SeMet/13_aod_semet_xyzout_prosmart_refmac-
> coot-2.pdb
Chain information for 13_aod_semet_xyzout_prosmart_refmac-coot-2.pdb #3
---
Chain | Description
A | No description available
B | No description available
124 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
6811 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
Computing secondary structure
> hide #!2 models
> hide #!3 models
> hide #!1 models
> show #!2 models
> ui tool show "Find Cavities"
> kvfinder #2
52 cavities found for AOD_TRS_refmac43-coot-2.pdb #2
AOD_TRS_refmac43-coot-2.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.2.29 | | 1620.22 | 1131.72 | 7501 | 14.71 | 3.33
2.2.7 | | 1569.89 | 1150.75 | 7268 | 14.82 | 3.4
2.2.38 | | 86.4 | 112.33 | 400 | 0 | 0
2.2.16 | | 82.73 | 111.95 | 383 | 0 | 0
2.2.27 | | 68.9 | 110.25 | 319 | 0 | 0
2.2.2 | | 57.46 | 58.54 | 266 | 2.55 | 0.86
2.2.39 | | 47.09 | 83.04 | 218 | 0 | 0
2.2.28 | | 39.31 | 49.37 | 182 | 3 | 1.01
2.2.30 | | 36.94 | 43.16 | 171 | 2.75 | 0.89
2.2.40 | | 34.99 | 45.7 | 162 | 2.16 | 0.54
2.2.14 | | 31.97 | 38.5 | 148 | 2.4 | 0.73
2.2.9 | | 30.67 | 50.75 | 142 | 0 | 0
2.2.44 | | 29.59 | 53.4 | 137 | 0 | 0
2.2.3 | | 28.73 | 37.99 | 133 | 1.7 | 0.57
2.2.49 | | 27.65 | 43.85 | 128 | 0 | 0
2.2.37 | | 27.22 | 43.99 | 126 | 0 | 0
2.2.25 | | 27 | 44.51 | 125 | 0 | 0
2.2.4 | | 24.84 | 44.52 | 115 | 0 | 0
2.2.26 | | 24.84 | 32.13 | 115 | 1.8 | 0.64
2.2.48 | | 24.19 | 43.26 | 112 | 0 | 0
2.2.1 | | 23.76 | 34.91 | 110 | 2.4 | 0.83
2.2.18 | | 22.9 | 40.08 | 106 | 0 | 0
2.2.52 | | 20.74 | 34.96 | 96 | 2.62 | 1.36
2.2.32 | | 19.87 | 36.19 | 92 | 0 | 0
2.2.51 | | 18.36 | 24.94 | 85 | 1.2 | 0.3
2.2.31 | | 17.93 | 34.52 | 83 | 1.2 | 0.25
2.2.13 | | 16.85 | 32.3 | 78 | 0 | 0
2.2.50 | | 15.77 | 26.05 | 73 | 1.8 | 0.72
2.2.22 | | 15.34 | 25.1 | 71 | 1.34 | 0.51
2.2.6 | | 15.12 | 24.19 | 70 | 1.8 | 0.62
2.2.10 | | 14.26 | 22.71 | 66 | 1.34 | 0.39
2.2.33 | | 13.39 | 25.5 | 62 | 1.9 | 0.7
2.2.47 | | 12.96 | 22.55 | 60 | 0.85 | 0.19
2.2.23 | | 12.53 | 23.49 | 58 | 1.34 | 0.43
2.2.8 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.11 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.19 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.20 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.36 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.45 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.43 | | 11.88 | 19.33 | 55 | 1.34 | 0.42
2.2.5 | | 11.66 | 14.92 | 54 | 0.85 | 0.27
2.2.35 | | 9.94 | 19.21 | 46 | 1.2 | 0.35
2.2.42 | | 9.29 | 18.69 | 43 | 1.04 | 0.41
2.2.21 | | 9.07 | 17.24 | 42 | 0.6 | 0.16
2.2.41 | | 8.86 | 14.92 | 41 | 0.6 | 0.22
2.2.17 | | 7.56 | 17.2 | 35 | 1.34 | 0.5
2.2.46 | | 7.34 | 14.05 | 34 | 1.04 | 0.37
2.2.34 | | 6.91 | 13.77 | 32 | 0.6 | 0.15
2.2.24 | | 6.48 | 12.18 | 30 | 0.6 | 0.18
2.2.15 | | 6.26 | 14.29 | 29 | 1.04 | 0.41
2.2.12 | | 5.83 | 13.68 | 27 | 0.85 | 0.31
> view #2.2.29 @< 3.5
> zoom 0.75
moved plane near -44.83356553534122 [ 0.26870197 0.53358857 -0.80192424]
moved plane far -44.83356553534122 [ 0.26870197 0.53358857 -0.80192424]
> surface #2.2.1-52 transparency 50
> ~surface #2.2
> surface #2.2.29
> show
> #!2/A:221-224,227,277-288/B:36-37,101,104-108,111-112,129,132-134,137,165-179,196,198-200,208,211,213,273,296,349-352,383,385-389,408,411-414
> view #!2.2.7 @< 3.5
> zoom 0.75
moved plane near -49.438209402625596 [ 0.6016213 0.78708752 -0.13618017]
moved plane far -49.438209402625596 [ 0.6016213 0.78708752 -0.13618017]
> ~surface #2.2
> surface #!2.2.7
> show
> #!2/A:36-37,101,105-108,111-112,129,132-134,137,164-179,198-200,205,208,211,213,273,296,349-352,381,383,385-389,408,411-414/B:221-224,226-227,277-288
> hide #!2 models
> show #!3 models
> ui tool show "Find Cavities"
> kvfinder #3
57 cavities found for 13_aod_semet_xyzout_prosmart_refmac-coot-2.pdb #3
13_aod_semet_xyzout_prosmart_refmac-coot-2.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
3.2.9 | | 1732.75 | 1207.55 | 8022 | 9.69 | 2.74
3.2.27 | | 1686.1 | 1191.88 | 7806 | 9.47 | 2.81
3.2.37 | | 95.47 | 120.86 | 442 | 0 | 0
3.2.12 | | 95.04 | 135.07 | 440 | 7.42 | 4.3
3.2.24 | | 69.34 | 104.11 | 321 | 0 | 0
3.2.3 | | 55.94 | 62.47 | 259 | 3.39 | 1.13
3.2.28 | | 46.22 | 67.51 | 214 | 0 | 0
3.2.39 | | 45.58 | 83.96 | 211 | 0 | 0
3.2.25 | | 41.26 | 46.95 | 191 | 2.75 | 0.91
3.2.23 | | 40.61 | 56.45 | 188 | 2.16 | 0.59
3.2.26 | | 38.45 | 50.58 | 178 | 3.06 | 1.16
3.2.53 | | 35.64 | 52.58 | 165 | 0 | 0
3.2.49 | | 35.21 | 55.64 | 163 | 0 | 0
3.2.11 | | 33.26 | 56.2 | 154 | 0 | 0
3.2.4 | | 32.4 | 43.46 | 150 | 2.08 | 0.66
3.2.16 | | 31.54 | 38.55 | 146 | 2.4 | 0.69
3.2.5 | | 27.86 | 47.94 | 129 | 0 | 0
3.2.18 | | 27.43 | 45.23 | 127 | 0 | 0
3.2.41 | | 27 | 34.27 | 125 | 1.9 | 0.6
3.2.56 | | 26.14 | 45.4 | 121 | 2.68 | 1.24
3.2.13 | | 25.7 | 43.88 | 119 | 3.06 | 1.21
3.2.32 | | 25.27 | 36.08 | 117 | 2.4 | 0.77
3.2.22 | | 24.84 | 44.52 | 115 | 0 | 0
3.2.31 | | 24.84 | 44.52 | 115 | 0 | 0
3.2.45 | | 24.84 | 44.52 | 115 | 0 | 0
3.2.40 | | 23.98 | 34.32 | 111 | 2.47 | 0.88
3.2.47 | | 22.46 | 35.7 | 104 | 0 | 0
3.2.55 | | 22.46 | 33.98 | 104 | 0.85 | 0.2
3.2.6 | | 19.87 | 36.19 | 92 | 0 | 0
3.2.36 | | 19.87 | 36.19 | 92 | 0 | 0
3.2.2 | | 19.66 | 31.1 | 91 | 2.47 | 1.06
3.2.19 | | 17.28 | 36.68 | 80 | 0 | 0
3.2.33 | | 17.28 | 26.31 | 80 | 1.2 | 0.28
3.2.7 | | 17.06 | 20.96 | 79 | 1.34 | 0.38
3.2.10 | | 16.85 | 32.3 | 78 | 0 | 0
3.2.14 | | 16.85 | 32.3 | 78 | 0 | 0
3.2.21 | | 15.77 | 24.69 | 73 | 1.7 | 0.62
3.2.30 | | 14.9 | 19.7 | 69 | 1.2 | 0.36
3.2.54 | | 14.69 | 21.56 | 68 | 1.8 | 0.51
3.2.17 | | 14.04 | 22.14 | 65 | 1.2 | 0.39
3.2.44 | | 12.96 | 18.98 | 60 | 1.2 | 0.32
3.2.15 | | 12.31 | 29.54 | 57 | 0 | 0
3.2.38 | | 12.31 | 29.54 | 57 | 0 | 0
3.2.46 | | 12.31 | 29.54 | 57 | 0 | 0
3.2.51 | | 12.31 | 29.54 | 57 | 0 | 0
3.2.52 | | 12.31 | 29.54 | 57 | 0 | 0
3.2.29 | | 11.02 | 19.76 | 51 | 0.6 | 0.19
3.2.43 | | 10.8 | 18.83 | 50 | 1.2 | 0.39
3.2.35 | | 9.29 | 17.23 | 43 | 1.34 | 0.45
3.2.20 | | 8.21 | 18.82 | 38 | 0.6 | 0.14
3.2.57 | | 8.21 | 18.94 | 38 | 1.34 | 0.47
3.2.1 | | 7.78 | 15.1 | 36 | 1.04 | 0.32
3.2.42 | | 7.78 | 12.72 | 36 | 0.6 | 0.2
3.2.8 | | 6.91 | 16.41 | 32 | 0.85 | 0.22
3.2.48 | | 6.7 | 12.19 | 31 | 0.85 | 0.32
3.2.50 | | 6.26 | 14.44 | 29 | 0.6 | 0.06
3.2.34 | | 5.18 | 11.25 | 24 | 0.6 | 0.02
> view #3.2.9 @< 3.5
> zoom 0.75
moved plane near -42.098697367909786 [ 0.79554454 0.54358023 -0.26763673]
moved plane far -42.098697367909786 [ 0.79554454 0.54358023 -0.26763673]
> surface #3.2.1-57 transparency 50
> ~surface #3.2
> surface #3.2.9
> show
> #!3/A:36-37,101,104-108,111-112,129,132-134,137,165-179,198-201,205,208,211,213,273-274,296,349-355,381,383,385-392,408,411-414/B:221-224,226-227,277-288
> hide #!1.2.1 models
> hide #!1.2.2 models
> hide #!1.2.3 models
> hide #!1.2.4 models
> hide #!1.2.5 models
> hide #!1.2.6 models
> hide #!1.2.7 models
> hide #!1.2.8 models
> hide #!1.2.9 models
> hide #!1.2.10 models
> hide #!1.2.11 models
> hide #!1.2.12 models
> hide #!1.2.13 models
> hide #!1.2.14 models
> hide #!1.2.15 models
> hide #!1.2.16 models
> hide #!1.2.17 models
> hide #!1.2.18 models
> hide #!1.2.19 models
> hide #!1.2.20 models
> hide #!1.2.21 models
> hide #!1.2.22 models
> hide #!1.2.23 models
> hide #!1.2.24 models
> hide #!1.2.47 models
> hide #!1.2.26 models
> hide #!1.2.27 models
> hide #!1.2.28 models
> hide #!1.2.29 models
> hide #!1.2.30 models
> hide #!1.2.31 models
> hide #!1.2.32 models
> hide #!1.2.33 models
> hide #!1.2.34 models
> hide #!1.2.36 models
> hide #!1.2.35 models
> hide #!1.2.37 models
> hide #!1.2.38 models
> hide #!1.2.39 models
> hide #!1.2.40 models
> hide #!1.2.41 models
> hide #!1.2.42 models
> hide #!1.2.43 models
> hide #!1.2.44 models
> hide #!1.2.45 models
> hide #!1.2.46 models
> hide #!3 models
> show #!1 models
> show #!1.2.8 models
> close #1.2.1-7
> view #!1.2.25 @< 3.5
> zoom 0.75
moved plane near -51.91654790357176 [-0.61186525 -0.78915603 -0.05341985]
moved plane far -51.91654790357176 [-0.61186525 -0.78915603 -0.05341985]
> ~surface #1.2
> surface #!1.2.25
> show
> #!1/A:101,105-108,111-112,129,133,165-178,198-201,205,208,211,213,273,296,349-353,381,383-389,391-392,408-414/B:222-225,227,277-281,283-288
> close #1.2.9-24
> view #!1.2.25 @< 3.5
> zoom 0.75
moved plane near -51.91654790357176 [-0.61186525 -0.78915603 -0.05341985]
moved plane far -51.91654790357176 [-0.61186525 -0.78915603 -0.05341985]
> ~surface #1.2
> surface #!1.2.25
> show
> #!1/A:101,105-108,111-112,129,133,165-178,198-201,205,208,211,213,273,296,349-353,381,383-389,391-392,408-414/B:222-225,227,277-281,283-288
> close #1.2.26-47
> view #!1.2.25 @< 3.5
> zoom 0.75
moved plane near -51.91654790357176 [-0.61186525 -0.78915603 -0.05341985]
moved plane far -51.91654790357176 [-0.61186525 -0.78915603 -0.05341985]
> ~surface #1.2
> surface #!1.2.25
> show
> #!1/A:101,105-108,111-112,129,133,165-178,198-201,205,208,211,213,273,296,349-353,381,383-389,391-392,408-414/B:222-225,227,277-281,283-288
> close #2.2.1-6
> view #!2.2.7 @< 3.5
> zoom 0.75
moved plane near -49.97603056990531 [-0.61186525 -0.78915603 -0.05341985]
moved plane far -49.97603056990531 [-0.61186525 -0.78915603 -0.05341985]
> ~surface #2.2
> surface #!2.2.7
> show
> #!2/A:36-37,101,105-108,111-112,129,132-134,137,164-179,198-200,205,208,211,213,273,296,349-352,381,383,385-389,408,411-414/B:221-224,226-227,277-288
> close #2.2.8-21
> view #!2.2.7 @< 3.5
> zoom 0.75
moved plane near -49.97603056990531 [-0.61186525 -0.78915603 -0.05341985]
moved plane far -49.97603056990531 [-0.61186525 -0.78915603 -0.05341985]
> ~surface #2.2
> surface #!2.2.7
> show
> #!2/A:36-37,101,105-108,111-112,129,132-134,137,164-179,198-200,205,208,211,213,273,296,349-352,381,383,385-389,408,411-414/B:221-224,226-227,277-288
> close #2.2.23-52
> view #!2.2.7 @< 3.5
> zoom 0.75
moved plane near -49.97603056990531 [-0.61186525 -0.78915603 -0.05341985]
moved plane far -49.97603056990531 [-0.61186525 -0.78915603 -0.05341985]
> ~surface #2.2
> surface #!2.2.7
> show
> #!2/A:36-37,101,105-108,111-112,129,132-134,137,164-179,198-200,205,208,211,213,273,296,349-352,381,383,385-389,408,411-414/B:221-224,226-227,277-288
> view #!2.2.7 @< 3.5
> zoom 0.75
moved plane near -49.97603056990531 [-0.61186525 -0.78915603 -0.05341985]
moved plane far -49.97603056990531 [-0.61186525 -0.78915603 -0.05341985]
> ~surface #2.2
> surface #!2.2.7
> show
> #!2/A:36-37,101,105-108,111-112,129,132-134,137,164-179,198-200,205,208,211,213,273,296,349-352,381,383,385-389,408,411-414/B:221-224,226-227,277-288
> show #!2 models
> hide #!1 models
> hide #!2.2.7 models
> show #!2.2.7 models
> hide #!2.2.22 models
> show #!2.2.22 models
> hide #!2.2.7 models
> hide #!2.2.22 models
> show #!2.2.22 models
> undo
[Repeated 8 time(s)]
> close #2.2
> ui tool show "Find Cavities"
> kvfinder #2
52 cavities found for AOD_TRS_refmac43-coot-2.pdb #2
AOD_TRS_refmac43-coot-2.pdb Cavities
---
ID | | Volume | Area | Points | Maximum
Depth | Average
Depth
2.2.29 | | 1620.22 | 1131.72 | 7501 | 14.71 | 3.33
2.2.7 | | 1569.89 | 1150.75 | 7268 | 14.82 | 3.4
2.2.38 | | 86.4 | 112.33 | 400 | 0 | 0
2.2.16 | | 82.73 | 111.95 | 383 | 0 | 0
2.2.27 | | 68.9 | 110.25 | 319 | 0 | 0
2.2.2 | | 57.46 | 58.54 | 266 | 2.55 | 0.86
2.2.39 | | 47.09 | 83.04 | 218 | 0 | 0
2.2.28 | | 39.31 | 49.37 | 182 | 3 | 1.01
2.2.30 | | 36.94 | 43.16 | 171 | 2.75 | 0.89
2.2.40 | | 34.99 | 45.7 | 162 | 2.16 | 0.54
2.2.14 | | 31.97 | 38.5 | 148 | 2.4 | 0.73
2.2.9 | | 30.67 | 50.75 | 142 | 0 | 0
2.2.44 | | 29.59 | 53.4 | 137 | 0 | 0
2.2.3 | | 28.73 | 37.99 | 133 | 1.7 | 0.57
2.2.49 | | 27.65 | 43.85 | 128 | 0 | 0
2.2.37 | | 27.22 | 43.99 | 126 | 0 | 0
2.2.25 | | 27 | 44.51 | 125 | 0 | 0
2.2.4 | | 24.84 | 44.52 | 115 | 0 | 0
2.2.26 | | 24.84 | 32.13 | 115 | 1.8 | 0.64
2.2.48 | | 24.19 | 43.26 | 112 | 0 | 0
2.2.1 | | 23.76 | 34.91 | 110 | 2.4 | 0.83
2.2.18 | | 22.9 | 40.08 | 106 | 0 | 0
2.2.52 | | 20.74 | 34.96 | 96 | 2.62 | 1.36
2.2.32 | | 19.87 | 36.19 | 92 | 0 | 0
2.2.51 | | 18.36 | 24.94 | 85 | 1.2 | 0.3
2.2.31 | | 17.93 | 34.52 | 83 | 1.2 | 0.25
2.2.13 | | 16.85 | 32.3 | 78 | 0 | 0
2.2.50 | | 15.77 | 26.05 | 73 | 1.8 | 0.72
2.2.22 | | 15.34 | 25.1 | 71 | 1.34 | 0.51
2.2.6 | | 15.12 | 24.19 | 70 | 1.8 | 0.62
2.2.10 | | 14.26 | 22.71 | 66 | 1.34 | 0.39
2.2.33 | | 13.39 | 25.5 | 62 | 1.9 | 0.7
2.2.47 | | 12.96 | 22.55 | 60 | 0.85 | 0.19
2.2.23 | | 12.53 | 23.49 | 58 | 1.34 | 0.43
2.2.8 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.11 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.19 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.20 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.36 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.45 | | 12.31 | 29.54 | 57 | 0 | 0
2.2.43 | | 11.88 | 19.33 | 55 | 1.34 | 0.42
2.2.5 | | 11.66 | 14.92 | 54 | 0.85 | 0.27
2.2.35 | | 9.94 | 19.21 | 46 | 1.2 | 0.35
2.2.42 | | 9.29 | 18.69 | 43 | 1.04 | 0.41
2.2.21 | | 9.07 | 17.24 | 42 | 0.6 | 0.16
2.2.41 | | 8.86 | 14.92 | 41 | 0.6 | 0.22
2.2.17 | | 7.56 | 17.2 | 35 | 1.34 | 0.5
2.2.46 | | 7.34 | 14.05 | 34 | 1.04 | 0.37
2.2.34 | | 6.91 | 13.77 | 32 | 0.6 | 0.15
2.2.24 | | 6.48 | 12.18 | 30 | 0.6 | 0.18
2.2.15 | | 6.26 | 14.29 | 29 | 1.04 | 0.41
2.2.12 | | 5.83 | 13.68 | 27 | 0.85 | 0.31
> close #2.2.1-6
> close #2.2.8-28
> close #2.2.30-52
> close #3.2.1-8
> view #!3.2.9 @< 3.5
> zoom 0.75
moved plane near -55.13919207738339 [ 0.73397596 0.64495711 -0.21286056]
moved plane far -55.13919207738339 [ 0.73397596 0.64495711 -0.21286056]
> ~surface #3.2
> surface #!3.2.9
> show
> #!3/A:36-37,101,104-108,111-112,129,132-134,137,165-179,198-201,205,208,211,213,273-274,296,349-355,381,383,385-392,408,411-414/B:221-224,226-227,277-288
> hide #2.1 models
> hide #!2.2 models
> hide #2.2.7 models
> hide #2.2.29 models
> show #2.2.29 models
> show #2.2.7 models
> hide #!2 models
> hide #!1 models
> close #3.2.10-26
> view #!3.2.9 @< 3.5
> zoom 0.75
moved plane near -55.13919207738339 [ 0.73397596 0.64495711 -0.21286056]
moved plane far -55.13919207738339 [ 0.73397596 0.64495711 -0.21286056]
> ~surface #3.2
> surface #!3.2.9
> show
> #!3/A:36-37,101,104-108,111-112,129,132-134,137,165-179,198-201,205,208,211,213,273-274,296,349-355,381,383,385-392,408,411-414/B:221-224,226-227,277-288
> close #3.2.28-57
> view #!3.2.9 @< 3.5
> zoom 0.75
moved plane near -55.13919207738339 [ 0.73397596 0.64495711 -0.21286056]
moved plane far -55.13919207738339 [ 0.73397596 0.64495711 -0.21286056]
> ~surface #3.2
> surface #!3.2.9
> show
> #!3/A:36-37,101,104-108,111-112,129,132-134,137,165-179,198-201,205,208,211,213,273-274,296,349-355,381,383,385-392,408,411-414/B:221-224,226-227,277-288
> show #!3 models
> show #!2 models
> show #!1 models
> save /home/maciek/Pulpit/Validation_AOD/AOD_cavities.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 255, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 384, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57':
Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57'
ValueError: error processing: 'tools' -> [, , , , , , ] -> -> 'cavity 57':
Error while saving session data for 'tools' -> [, , , , , , ] -> -> 'cavity
57'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 255, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 384, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 133, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 68, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57':
Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57'
ValueError: error processing: 'tools' -> [, , , , , , ] -> -> 'cavity 57':
Error while saving session data for 'tools' -> [, , , , , , ] -> -> 'cavity
57'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
> save /home/maciek/Pulpit/Validation_AOD/cav.cxs
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 255, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 384, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57':
Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57'
ValueError: error processing: 'tools' -> [, , , , , , ] -> -> 'cavity 57':
Error while saving session data for 'tools' -> [, , , , , , ] -> -> 'cavity
57'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 322, in process
data = sm.take_snapshot(obj, session, self.state_flags)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/structure.py", line 255, in take_snapshot
data = {'model state': Model.take_snapshot(self, session, flags),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/models.py", line 384, in take_snapshot
'positions': self.positions.array(),
^^^^^^^^^^^^^^^^^^^^
AttributeError: 'NoneType' object has no attribute 'array'
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 297, in discovery
self.processed[key] = self.process(obj, parents)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 329, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/tool.py", line 185, in callback
bundle_info.run_provider(session, name, session.toolbar,
display_name=display_name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/info.py", line 397, in run_provider
return api._api_caller.run_provider(api, session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/toolshed/__init__.py", line 1420, in run_provider
return cls._get_func(api, "run_provider")(session, name, mgr, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/__init__.py", line 37, in run_provider
providers.run_provider(session, name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/providers.py", line 56, in run_provider
what(session)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/toolbar/providers.py", line 38, in _file_save
show_save_file_dialog(session)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 144, in show_save_file_dialog
_dlg.display(session, **kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/dialog.py", line 68, in display
run(session, cmd)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 86, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3237, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/save_command/cmd.py", line 101, in provider_save
saver_info.save(session, path, **provider_kw)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core_formats/__init__.py", line 95, in save
return cxs_save(session, path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 1048, in save
session.save(output, version=version, include_maps=include_maps)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 731, in save
mgr.discovery(self._state_containers)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
ValueError: error processing: 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57':
Error while saving session data for 'tools' ->
[<chimerax.model_panel.tool.ModelPanel object at 0x7e751aa81610>,
<chimerax.toolbar.tool.ToolbarTool object at 0x7e7477f4d850>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e745e00e290>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e743d0c71d0>,
<chimerax.log.tool.Log object at 0x7e74b0445cd0>,
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910>,
<chimerax.cmd_line.tool.CommandLine object at 0x7e74b0480b50>] ->
<chimerax.kvfinder.tool.KVFinderResultsDialog object at 0x7e7392867910> ->
<chimerax.atomic.structure.Structure object at 0x7e73c80c0510> 'cavity 57'
ValueError: error processing: 'tools' -> [, , , , , , ] -> -> 'cavity 57':
Error while saving session data for 'tools' -> [, , , , , , ] -> -> 'cavity
57'
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/session.py", line 301, in discovery
raise ValueError(
See log for complete Python traceback.
OpenGL version: 4.6 (Core Profile) Mesa 25.0.7-0ubuntu0.24.04.2
OpenGL renderer: Mesa Intel(R) Graphics (RPL-S)
OpenGL vendor: Intel
Python: 3.11.13
Locale: en_GB.UTF-8
Qt version: PyQt6 6.9.1, Qt 6.9.0
Qt runtime version: 6.9.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: LENOVO
Model: 83DG
OS: Ubuntu 24.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 Intel(R) Core(TM) i7-14650HX
Cache Size: 30720 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 7.3Gi 8.0Gi 1.3Gi 17Gi 23Gi
Swap: 8.0Gi 512Ki 8.0Gi
Graphics:
00:02.0 VGA compatible controller [0300]: Intel Corporation Raptor Lake-S UHD Graphics [8086:a78b] (rev 04)
Subsystem: Lenovo Raptor Lake-S UHD Graphics [17aa:3e45]
Kernel driver in use: i915
Installed Packages:
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.11.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 25.4.0
autocommand: 2.2.2
babel: 2.17.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 3.11.1
build: 1.3.0
certifi: 2025.11.12
cftime: 1.6.5
charset-normalizer: 3.4.4
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.1.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.61.4
ChimeraX-AtomicLibrary: 14.2.1
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.3
ChimeraX-Clipper: 0.23.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.0
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.11rc202511260300
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.4
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.7.2
ChimeraX-Label: 1.2
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.2
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.2.2
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.1.0
ChimeraX-MDcrds: 2.17.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.2
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.22
ChimeraX-ModelPanel: 1.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.2
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.11
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.4.1
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.5
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.10
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.17.3
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.2
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.49.1
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.5.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.3.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.12.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.1.4
debugpy: 1.8.17
decorator: 5.2.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.60.1
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.15.1
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.11
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 1.4.1
importlib_metadata: 8.0.0
inflect: 7.3.1
iniconfig: 2.3.0
ipykernel: 6.30.1
ipython: 9.5.0
ipython_pygments_lexers: 1.1.1
ipywidgets: 8.1.8
jaraco.collections: 5.1.0
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.25.1
jsonschema-specifications: 2025.9.1
jupyter_client: 8.6.3
jupyter_core: 5.9.1
jupyterlab_widgets: 3.0.16
kiwisolver: 1.4.9
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.1
mcp: 1.18.0
more-itertools: 10.3.0
msgpack: 1.1.1
multidict: 6.7.0
narwhals: 2.13.0
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 2.3.5
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.2.0
OpenMM-CUDA-12: 8.2.0
openvr: 1.26.701
packaging: 25.0
packaging: 24.2
ParmEd: 4.2.2
parso: 0.8.5
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.5.0
platformdirs: 4.2.2
plotly: 6.5.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.4.1
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.12.5
pydantic-settings: 2.12.0
pydantic_core: 2.41.5
pydicom: 2.4.4
Pygments: 2.18.0
pyKVFinder: 0.8.4
pynmrstar: 3.3.6
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.2.5
pyproject_hooks: 1.2.0
PyQt6: 6.9.1
PyQt6-Qt6: 6.9.2
PyQt6-WebEngine: 6.9.0
PyQt6-WebEngine-Qt6: 6.9.2
PyQt6_sip: 13.10.2
pytest: 9.0.1
pytest-cov: 7.0.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.1
python-multipart: 0.0.20
pytz: 2025.2
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals-py: 3.1.0
rpds-py: 0.29.0
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
sniffio: 1.3.1
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8
Sphinx: 8.2.3
sphinx-autodoc-typehints: 3.2.0
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.0.3
stack-data: 0.6.3
starlette: 0.50.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 1.5.1
tifffile: 2025.3.13
tinyarray: 1.2.5
tomli: 2.0.1
tomlkit: 0.13.3
tornado: 6.5.2
traitlets: 5.14.3
typeguard: 4.3.0
typing-inspection: 0.4.2
typing_extensions: 4.15.0
typing_extensions: 4.12.2
tzdata: 2025.2
urllib3: 2.5.0
uvicorn: 0.38.0
wcwidth: 0.2.14
webcolors: 24.11.1
wheel: 0.45.1
wheel: 0.45.1
wheel-filename: 1.4.2
widgetsnbextension: 4.0.15
yarl: 1.22.0
zipp: 3.19.2
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