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Opened 2 years ago
Closed 2 years ago
#9696 closed defect (fixed)
restore_snapshot for "Volume" returned None
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Linux-5.19.0-50-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Preliminary_figures/Supplementary_material/SF3_Asc1_TMs/local_res_TMs.cxs
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
restore_snapshot for "Volume" returned None
restore_snapshot for "VolumeSurface" returned None
Opened noise_suppressed.mrc copy as #4, grid size 600,600,600, pixel 0.415,
shown at level 0.01, step 1, values float32
Unable to restore session, resetting.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/core/session.py", line 734, in restore
obj = sm.restore_snapshot(self, data)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/colorvol.py", line 415, in restore_snapshot
c.set_vertex_colors()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/colorvol.py", line 239, in set_vertex_colors
s.vertex_colors = self.vertex_colors(report_stats)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/colorvol.py", line 211, in vertex_colors
values, outside = self.volume_values()
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/colorvol.py", line 276, in volume_values
return self.offset_values(v, n, tf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/colorvol.py", line 308, in offset_values
values, outside = self.vertex_values(vo, xf)
File "/usr/lib/ucsf-chimerax/lib/python3.9/site-
packages/chimerax/surface/colorvol.py", line 317, in vertex_values
values, outside = v.interpolated_values(vertices, vertex_xform,
AttributeError: 'NoneType' object has no attribute 'interpolated_values'
Log from Tue Mar 14 08:52:57 2023UCSF ChimeraX version: 1.5rc202211091945
(2022-11-09)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Supplementary_material/Asc1_TMs/local_res_TMs.cxs
> format session
Opened noise_suppressed.mrc as #1, grid size 600,600,600, pixel 0.415, shown
at level 0.01, step 1, values float32
Opened noise_suppressed.mrc copy as #4, grid size 600,600,600, pixel 0.415,
shown at level 0.01, step 1, values float32
Opened
cryosparc_P4_J852_005_volume_map_half_B_and_cryosparc_P4_J852_005_volume_map_half_A_local_resolution.ccp4
as #3, grid size 300,300,300, pixel 0.831, shown at level 10.1, step 2, values
float32
Log from Tue Mar 14 08:51:13 2023UCSF ChimeraX version: 1.5rc202211091945
(2022-11-09)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/local_resolution/local_res_detail.cxs
> format session
Opened noise_suppressed.mrc as #1, grid size 600,600,600, pixel 0.415, shown
at level 0.01, step 1, values float32
Opened noise_suppressed.mrc copy as #4, grid size 600,600,600, pixel 0.415,
shown at level 0.01, step 1, values float32
Opened
cryosparc_P4_J852_005_volume_map_half_B_and_cryosparc_P4_J852_005_volume_map_half_A_local_resolution.ccp4
as #3, grid size 300,300,300, pixel 0.831, shown at level 10.1, step 2, values
float32
Log from Fri Mar 10 16:48:37 2023UCSF ChimeraX version: 1.5rc202211091945
(2022-11-09)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/local_resolution/LocalResolution_2/local_res.cxs
> format session
Opened noise_suppressed.mrc as #1, grid size 600,600,600, pixel 0.415, shown
at level 0.01, step 1, values float32
Opened noise_suppressed.mrc copy as #4, grid size 600,600,600, pixel 0.415,
shown at level 0.01, step 1, values float32
Opened
cryosparc_P4_J852_005_volume_map_half_B_and_cryosparc_P4_J852_005_volume_map_half_A_local_resolution.ccp4
as #3, grid size 300,300,300, pixel 0.831, shown at level 10.1, step 2, values
float32
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Log from Fri Mar 3 16:07:40 2023UCSF ChimeraX version: 1.5rc202211091945
(2022-11-09)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/Asc1_model_rainbow.cxs
> format session
Opened noise_suppressed.mrc as #1, grid size 600,600,600, pixel 0.415, shown
at level 0.01, step 1, values float32
Opened noise_suppressed.mrc copy as #4, grid size 600,600,600, pixel 0.415,
shown at level 0.01, step 1, values float32
Log from Mon Feb 20 16:53:59 2023UCSF ChimeraX version: 1.5rc202211091945
(2022-11-09)
© 2016-2022 Regents of the University of California. All rights reserved.
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/Asc1_model_rainbow.cxs
> format session
Opened noise_suppressed.mrc as #1, grid size 600,600,600, pixel 0.415, shown
at level 0.0132, step 1, values float32
Log from Fri Feb 17 11:48:40 2023You can double click a model's Name or ID in
the model panel to edit those fields
UCSF ChimeraX version: 1.5rc202211091945 (2022-11-09)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/noise_suppressed.mrc
Opened noise_suppressed.mrc as #1, grid size 600,600,600, pixel 0.415, shown
at level 0.00272, step 4, values float32
> volume #1 step 1
> volume #1 level 0.01193
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/refined_17_final.pdb
Chain information for refined_17_final.pdb #2
---
Chain | Description
A | No description available
B | No description available
> set bgColor white
> hide #!1 models
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> rainbow
> select /B
3759 atoms, 3851 bonds, 477 residues, 1 model selected
> color sel hot pink
> color sel magenta
> select clear
> select ::name="AJP"::name="BMA"::name="NAG"
194 atoms, 208 bonds, 9 residues, 1 model selected
> color sel orange red
> color sel byhetero
> select clear
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/Asc1_model_rainbow.cxs
> show #!1 models
> color bychain
> rainbow
> show surfaces
> rainbow
> volume #1 level 0.01325
> hide #!1 models
> hide surfaces
> show #!1 models
> hide #!1 models
> select /B
3759 atoms, 3851 bonds, 477 residues, 1 model selected
> color (#!2 & sel) magenta
> select ::name="AJP"::name="BMA"::name="NAG"
194 atoms, 208 bonds, 9 residues, 1 model selected
> color sel orange red
> color sel byhetero
> select clear
> select #3:154.A,109.B
Expected an objects specifier or a keyword
> select #2:154.A,109.B
Expected an objects specifier or a keyword
> select #2: 154.A,109.B
Expected an objects specifier or a keyword
> select #2: 154.A, 109.B
Expected an objects specifier or a keyword
> select #2: 154.A, 109.B
Expected an objects specifier or a keyword
> select #2:154.A
Expected an objects specifier or a keyword
> select sequence 154.A
Nothing selected
> select sequence 154
Nothing selected
> select #2:154.A
Expected an objects specifier or a keyword
> select #2:A.154
Expected an objects specifier or a keyword
> select add #2
7306 atoms, 7509 bonds, 927 residues, 1 model selected
> select clear
> select /A:154
6 atoms, 5 bonds, 1 residue, 1 model selected
> select clear
> select /A:154
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:154,/B:109
Expected an objects specifier or a keyword
> select /A:154, /B:109
Expected an objects specifier or a keyword
> select /B:109
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A:154
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /B:109
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /A:154
12 atoms, 10 bonds, 2 residues, 2 models selected
> show (#!2 & sel) target ab
> color (#!2 & sel) byhetero
> select clear
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/Asc1_model_rainbow.cxs
> lighting full
> lighting soft
> lighting simple
> show #!1 models
> ui tool show "Color Zone"
> ui tool show "Segment Map"
Segmenting noise_suppressed.mrc, density threshold 0.013247
Only showing 60 of 315 regions.
Showing 60 of 315 region surfaces
733 watershed regions, grouped to 315 regions
Showing noise_suppressed.seg - 315 regions, 60 surfaces
Ungrouped to 233 regions, but did not show all surfaces, see Options
Segmenting noise_suppressed.mrc, density threshold 0.013247
Only showing 60 of 315 regions.
Showing 60 of 315 region surfaces
733 watershed regions, grouped to 315 regions
Showing noise_suppressed.seg - 315 regions, 60 surfaces
Segmenting noise_suppressed.mrc, density threshold 0.013247
Only showing 60 of 154 regions.
Showing 60 of 154 region surfaces
733 watershed regions, grouped to 154 regions
Showing noise_suppressed.seg - 154 regions, 60 surfaces
> hide #3.17 models
> show #3.17 models
> hide #3.16 models
> show #3.16 models
> hide #3.15 models
> show #3.15 models
> hide #!1 models
> hide #!2 models
> show #!2 models
> hide #3.1 models
> hide #3.2 models
> select #3.58
1 model selected
> select add #3.27
2 models selected
> select add #3.6
3 models selected
> select add #3.32
4 models selected
> select add #3.26
5 models selected
> select add #3.8
6 models selected
> select add #3.43
7 models selected
> select add #3.29
8 models selected
> select add #3.36
9 models selected
> select add #3.37
10 models selected
> hide #3.32 models
> hide #3.36 models
> hide #3.37 models
> hide #3.43 models
> hide #3.58 models
> hide #3.29 models
> hide #3.27 models
> hide #3.26 models
> hide #3.8 models
> show #3.1 models
> hide #!3 models
> hide #!2 models
> show #!1 models
> hide #!1 models
> show #!2 models
> ui mousemode right zoom
> show #!3 models
> show #3.2 models
> show #3.8 models
> hide #3.8 models
> show #3.8 models
> hide #3.2 models
> show #3.2 models
> hide #3.1 models
> show #3.1 models
> select clear
Drag select of 1311, 654721 of 714812 triangles, 953, 623, 583, 681, 928, 468,
574, 700, 725, 670, 138 atoms, 412 residues, 140 bonds
> hide #!2 models
> select clear
> hide #3.1 models
> show #3.1 models
> hide #3.2 models
> show #!2 models
> select add #3.48
1 model selected
> select add #3.20
2 models selected
> select add #3.41
3 models selected
> select add #3.11
4 models selected
> select add #3.22
5 models selected
> select add #3.1
6 models selected
> select add #3.13
7 models selected
> select subtract #3.13
6 models selected
> hide #!2 models
> select add #3.18
7 models selected
> select add #3.54
8 models selected
> select subtract #3.54
7 models selected
> select subtract #3.18
6 models selected
> select add #3.18
7 models selected
> select add #3.19
8 models selected
> select subtract #3.19
7 models selected
> select add #3.53
8 models selected
> select add #3.12
9 models selected
> select add #3.13
10 models selected
> hide #3.3 models
> show #3.3 models
> hide #3.3 models
> hide #3.4 models
> show #3.4 models
> hide #3.4 models
> hide #3.5 models
> hide #3.6 models
> show #3.5 models
> hide #3.5 models
> hide #3.7 models
> hide #3.8 models
> show #3.8 models
> hide #3.8 models
> hide #3.9 models
> show #3.9 models
> show #!2 models
> hide #3.9 models
> hide #3.10 models
> hide #3.11 models
> show #3.11 models
> hide #3.12 models
> show #3.12 models
> hide #3.12 models
> show #3.12 models
> hide #3.13 models
> show #3.13 models
> hide #3.13 models
> show #3.13 models
> hide #3.13 models
> show #3.13 models
> hide #3.14 models
> show #3.14 models
> hide #3.14 models
> hide #3.15 models
> hide #3.16 models
> hide #3.17 models
> hide #3.19 models
> hide #3.21 models
> hide #3.23 models
> hide #3.24 models
> hide #3.25 models
> hide #3.28 models
> hide #3.30 models
> hide #3.31 models
> hide #3.33 models
> hide #3.34 models
> hide #3.35 models
> hide #3.38 models
> hide #3.39 models
> hide #3.40 models
> hide #3.42 models
> hide #3.44 models
> hide #3.45 models
> hide #3.46 models
> hide #3.47 models
> hide #3.49 models
> hide #3.50 models
> hide #3.51 models
> hide #3.52 models
> hide #3.54 models
> hide #3.55 models
> hide #3.56 models
> hide #3.57 models
> hide #3.59 models
> hide #3.60 models
> close #3
> show #!1 models
Segmenting noise_suppressed.mrc, density threshold 0.013247
Only showing 60 of 363 regions.
Showing 60 of 363 region surfaces
733 watershed regions, grouped to 363 regions
Showing noise_suppressed.seg - 363 regions, 60 surfaces
> close #3
Segmenting noise_suppressed.mrc, density threshold 0.013247
Only showing 2 of 363 regions.
Showing 2 of 363 region surfaces
733 watershed regions, grouped to 363 regions
Showing noise_suppressed.seg - 363 regions, 2 surfaces
> hide #3.1 models
> show #3.1 models
> hide #!3 models
> hide #!1 models
> hide #3.1 models
> show #3.1 models
> hide #3.2 models
> show #3.2 models
> hide #!3 models
> show #!3 models
> close #3
Segmenting noise_suppressed.mrc, density threshold 0.013247
Only showing 2 of 154 regions.
Showing 2 of 154 region surfaces
733 watershed regions, grouped to 154 regions
Showing noise_suppressed.seg - 154 regions, 2 surfaces
> show #!1 models
> hide #3.2 models
> hide #3.1 models
> hide #!3 models
> rainbow
> undo
> color zone #1 near #2 distance 2.49
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/Asc1_model_rainbow.cxs
——— End of log from Fri Feb 17 11:48:40 2023 ———
opened ChimeraX session
Showing noise_suppressed.seg - 154 regions, 2 surfaces
> close #3
> volume #1 level 0.00851
> volume #1 level 0.009826
> hide #!1 models
> select ::name="AJP"::name="BMA"::name="NAG"
194 atoms, 208 bonds, 9 residues, 1 model selected
> color sel orange
> color sel orange red
> select clear
> select /A:154
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add /B:109
12 atoms, 10 bonds, 2 residues, 2 models selected
> hide (#!2 & sel) target a
> select clear
> show #!1 models
> surface dust #1 size 4.15
> ui tool show "Hide Dust"
> surface dust #1 size 14.9
> surface dust #1 size 19.47
> hide #!2 models
> show #!2 models
> hide #!1 models
> show #!1 models
> color zone #1 near #2 distance 2.49
> volume #1 level 0.01062
> volume #1 level 0.009036
> volume #1 level 0.009
> volume #1 level 0.0098
> volume #1 level 0.01
> surface dust #1 size 20.47
> surface dust #1 size 21.47
> surface dust #1 size 22.47
> surface dust #1 size 25.01
[Repeated 1 time(s)]
> surface dust #1 size 95.34
> surface dust #1 size 22.63
> surface dust #1 size 23.8
> ui tool show "Color Zone"
> color zone #1 near #2 distance 7.88
> color zone #1 near #2 distance 7.78
> color zone #1 near #2 distance 6.66
> surface dust #1 size 49.67
[Repeated 1 time(s)]
> surface dust #1 size 82.01
> surface dust #1 size 100.27
> surface dust #1 size 110.27
> surface dust #1 size 120.27
> surface dust #1 size 130.27
> surface dust #1 size 140.27
> surface dust #1 size 130.27
> surface dust #1 size 120.27
> volume #1 level 0.012
> volume #1 level 0.011
> volume #1 level 0.01
> volume #1 level 0.0105
> volume #1 level 0.0102
> color zone #1 near #2 distance 2.49
> color zone #1 near #2 distance 9.14
> color zone #1 near #2 distance 9.08
> color zone #1 near #2 distance 9.02
> color zone #1 near #2 distance 8.96
> color zone #1 near #2 distance 19.97
> color zone #1 near #2 distance 19.83
> color zone #1 near #2 distance 18.83
> volume #1 level 0.009
> color zone #1 near #2 distance 21.92
> surface dust #1 size 135.51
> surface dust #1 size 122.51
> surface dust #1 size 10
> surface dust #1 size 100
[Repeated 1 time(s)]
> surface dust #1 size 10
> surface dust #1 size 110
[Repeated 1 time(s)]
> surface dust #1 size 10
> surface dust #1 size 120
[Repeated 1 time(s)]
> surface dust #1 size 10
> surface dust #1 size 130
[Repeated 1 time(s)]
> surface dust #1 size 10
> surface dust #1 size 120
[Repeated 1 time(s)]
> surface dust #1 size 12
> surface dust #1 size 125
[Repeated 1 time(s)]
> surface dust #1 size 12
> surface dust #1 size 122
[Repeated 1 time(s)]
> surface dust #1 size 12
> surface dust #1 size 120
[Repeated 1 time(s)]
> surface dust #1 size 12
> surface dust #1 size 121
[Repeated 1 time(s)]
> surface dust #1 size 1
> surface dust #1 size 12
> surface dust #1 size 122
[Repeated 1 time(s)]
> surface dust #1 size 112
> surface dust #1 size 122
> surface dust #1 size 12
> surface dust #1 size 121
[Repeated 1 time(s)]
> color zone #1 near #2 distance 20.92
> surface dust #1 size 121
> volume #1 level 0.007684
> volume #1 level 0.01
> volume #1 level 0.009
> volume #1 level 0.012
> volume #1 level 0.011
> volume #1 level 0.0105
> volume #1 level 0.012
> volume #1 level 0.011
> volume #1 level 0.01
> volume #1 level 0.0105
> volume #1 level 0.01
> color zone #1 near #2 distance 19.92
> color zone #1 near #2 distance 18.92
> color zone #1 near #2 distance 1
> color zone #1 near #2 distance 15
[Repeated 1 time(s)]
> hide #!2 models
> color zone #1 near #2 distance 1
> color zone #1 near #2 distance 12
[Repeated 1 time(s)]
> color zone #1 near #2 distance 1
> color zone #1 near #2 distance 10
> color zone #1 near #2 distance 1
> color zone #1 near #2 distance 8
[Repeated 1 time(s)]
> color zone #1 near #2 distance 5
[Repeated 1 time(s)]
> color zone #1 near #2 distance 8
[Repeated 1 time(s)]
> color zone #1 near #2 distance 7
[Repeated 1 time(s)]
> color zone #1 near #2 distance 6
[Repeated 1 time(s)]
> color zone #1 near #2 distance 7
> color zone #1 near #2 distance 7.5
> color zone #1 near #2 distance 80
> color zone #1 near #2 distance 8
[Repeated 1 time(s)]
> color zone #1 near #2 distance 9
[Repeated 1 time(s)]
> lighting shadows true
> lighting full
> lighting soft
> lighting simple
> lighting soft
> ui tool show "Map Eraser"
> view
> ui mousemode right select
> ui mousemode right rotate
> ui mousemode right "map eraser"
> volume copy #1 subregion 323,342,262,334,353,273
Opened noise_suppressed.mrc copy as #4, grid size 12,12,12, pixel 0.415, shown
at step 1, values float32
> undo
[Repeated 3 time(s)]
> close #3
> show #!1 models
> show #!2 models
> hide #!4 models
> hide #3 models
> close #3
> show #!4 models
> hide #!4 models
> close #4
> volume erase #1 center 136.81,144.71,111.12 radius 1.994
Opened noise_suppressed.mrc copy as #4, grid size 600,600,600, pixel 0.415,
shown at step 1, values float32
> volume erase #4 center 139.4,144.22,109.63 radius 1.994
> show #!1 models
> hide #3 models
> hide #!2 models
> show #3 models
> show #!2 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 1 atomic
models, 2 maps.
> hide #!4 models
> show #!4 models
> hide #!1 models
> color zone #4 near #2 distance 2.49
> surface dust #1 size 121
> surface dust #4 size 120
> color zone #4 near #2 distance 8
[Repeated 1 time(s)]
> volume erase #4 center 123.08,104.44,141.64 radius 2.8608
> volume erase #4 center 131.61,141.49,116.88 radius 2.4401
> volume erase #4 center 110.8,125.68,116.6 radius 1.9353
> volume erase #4 center 116.31,136.97,112.93 radius 2.4401
> volume erase #4 center 113.28,137.26,115.28 radius 2.4401
> volume erase #4 center 114.06,133.03,116.31 radius 2.5242
> ui mousemode right select
> ui mousemode right rotate
> color zone #4 near #2 distance 8.1
> color zone #4 near #2 distance 8.2
> color zone #4 near #2 distance 8.3
> color zone #4 near #2 distance 8.4
> color zone #4 near #2 distance 8.5
> color zone #4 near #2 distance 8.6
> color zone #4 near #2 distance 8.7
> color zone #4 near #2 distance 8.8
> color zone #4 near #2 distance 8.9
> color zone #4 near #2 distance 9
> hide #!2 models
> hide #!4 models
> show #!2 models
Drag select of 243 atoms, 918 residues, 251 bonds
> hide (#!2 & sel) target a
> show #!4 models
> color zone #4 near sel & #2 distance 2.49
> undo
> select clear
> hide #!4 models
Drag select of 918 residues
> color (#!2 & sel) byhetero
> select ::name="AJP"::name="BMA"::name="NAG"
194 atoms, 208 bonds, 9 residues, 1 model selected
> show sel target ab
> select clear
> select #2 \B:264,280,323,405
Expected a keyword
> select #2\B:264,280,323,405
Expected an objects specifier or a keyword
> select #2/B:264,280,323,405
32 atoms, 28 bonds, 4 residues, 1 model selected
> show (#!2 & sel) target ab
> color (#!2 & sel) magenta
> select clear
> show #!4 models
> color zone #4 near #2 distance 2.49
> hide #!2 models
Color zone shortcut requires 1 displayed atomic model and 1 map, got 0 atomic
models, 1 maps.
> hide #!4 models
> show #!2 models
> show #!4 models
> hide #!2 models
> hide #!4 models
> show #!2 models
> hide #2 target a
> undo
> show #!4 models
> ui tool show "Color Actions"
> color hetero
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> ui tool show "Color Actions"
> color bychain
[Repeated 1 time(s)]
> color zone #4 near #2 distance 2.49
> ui tool show "Color Actions"
> color rainbow
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> rainbow
> color zone #4 near #2 distance 2.49
> color zone #4 near #2 distance 9
> select /B
3759 atoms, 3851 bonds, 477 residues, 1 model selected
> color (#!2 & sel) magenta
> color zone #4 near sel & #2 distance 2.49
[Repeated 1 time(s)]
> select clear
> color zone #4 near #2 distance 2.49
> color zone #4 near #2 distance 9
> select ::name="AJP"::name="BMA"::name="NAG"
194 atoms, 208 bonds, 9 residues, 1 model selected
> color sel orange red
> color zone #4 near sel & #2 distance 2.49
> select clear
> color zone #4 near #2 distance 2.49
> color zone #4 near #2 distance 9
> color zone #4 near #2 distance 1
> color zone #4 near #2 distance 10
[Repeated 1 time(s)]
> hide #!2 models
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/Asc1_model_rainbow.cxs
——— End of log from Mon Feb 20 16:53:59 2023 ———
opened ChimeraX session
> show #!2 models
> show #!1 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!1 models
> color zone #4 near #2 distance 2.49
> ui tool show "Color Zone"
> color zone #4 near #2 distance 3.34
> color zone #4 near #2 distance 52.6
> hide #!2 models
> show #!2 models
> hide #!4 models
> nucleotides fill
> style nucleic stick
Changed 0 atom styles
> nucleotides atoms
> style nucleic stick
Changed 0 atom styles
> nucleotides ladder
> preset "overall look" "publication 1 (silhouettes)"
Using preset: Overall Look / Publication 1 (Silhouettes)
Preset expands to these ChimeraX commands:
set bg white
graphics silhouettes t
lighting depthCue f
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting simple
> lighting shadows true
> lighting shadows false
> show #!4 models
> hide #!4 models
> select #2/A:154,B:109
18 atoms, 17 bonds, 2 residues, 1 model selected
> select add /B:109
24 atoms, 22 bonds, 3 residues, 2 models selected
> show (#!2 & sel) target ab
> color (#!2 & sel) byhetero
> select clear
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!2 models
> lighting shadows true
> lighting shadows false
> lighting full
> save /home/mmartinezm/Desktop/image7.png supersample 3
> show #!2 models
> hide #!4 models
> lighting shadows false
> lighting shadows true
> lighting flat
[Repeated 1 time(s)]
> lighting full
> lighting soft
> lighting full
> lighting shadows false
> graphics silhouettes false
> lighting shadows true
> lighting simple
> lighting full
[Repeated 1 time(s)]
> lighting flat
> lighting full
> lighting shadows false
> save /home/mmartinezm/Desktop/image8.png supersample 3
> show #!4 models
> hide #!2 models
> save /home/mmartinezm/Desktop/image9.png supersample 3
> show #!2 models
> hide #!4 models
> save /home/mmartinezm/Desktop/image10.png supersample 3
> show #!4 models
> ui tool show "Surface Color"
> open
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/local_resolution/LocalResolution_2/cryosparc_P4_J852_005_volume_map_half_B_and_cryosparc_P4_J852_005_volume_map_half_A_local_resolution.ccp4
Opened
cryosparc_P4_J852_005_volume_map_half_B_and_cryosparc_P4_J852_005_volume_map_half_A_local_resolution.ccp4
as #3, grid size 300,300,300, pixel 0.831, shown at level 10.1, step 2, values
float32
> hide #!4 models
> show #!4 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> color electrostatic #4.1 map #3 palette -10,#ff0000:0,#ffffff:10,#0000ff
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
> color electrostatic #4.1 map #3 palette
> 3.4,#ff0000:3.8,#ffcb00:4,#66ff00:4.5,#00ff65:5,#00ccff:5.3,#0000ff
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
> hide #!2 models
> key red:3.4 #ffcb00:3.8 #66ff00:4.0 #00ff65:4.5 #00ccff:5.0 blue:5.3
> showTool true
> ui mousemode right "color key"
> key pos 0.88961,0.123288 size 0.038961,0.32005
> key fontSize 23
> key fontSize 22
> key fontSize 21
> key fontSize 20
> key fontSize 19
> key fontSize 18
> key fontSize 17
> key fontSize 16
> ui mousemode right translate
> save /home/mmartinezm/Desktop/image11.png supersample 3
> save /home/mmartinezm/Desktop/image12.png supersample 3
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/local_resolution/LocalResolution_2/local_res.cxs
——— End of log from Fri Mar 3 16:07:40 2023 ———
opened ChimeraX session
> hide #!4 models
> hide #5 models
> show #!1 models
Drag select of 1 noise_suppressed.mrc
> color #1 #86b58dff models
> color #1 plum models
> select clear
> transparency #1.1 50
> transparency #1.1 0
> lighting shadows true
> lighting shadows false
> lighting flat
> lighting full
> lighting shadows false
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> volume #1 level 0.008565
> volume #1 level 0.001
> volume #1 level 0.01
> save /home/mmartinezm/Desktop/image1.png supersample 3
> hide #!1 models
> show #!4 models
> show #!3 models
> hide #!3 models
> show #!3 models
> hide #!3 models
> ui tool show "Surface Color"
> color electrostatic #4.1 map #3 palette
> 3.4,#ff0000:3.8,#ffcb00:4,#66ff00:4.5,#00ff65:5,#00ccff:5.3,#0000ff
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
> ui tool show "Side View"
> color electrostatic #4.1 map #3 palette
> 3.9,#ff0000:4.1,#ffcb00:4.3,#66ff00:4.5,#00ff65:51,#00ccff:5.3,#0000ff
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.473, mean 3.951, maximum 5.034
> color electrostatic #4.1 map #3 palette
> 3.9,#ff0000:4.1,#ff6666:4.3,#ffcccc:4.5,#cbcbff:51,#6565ff:5.3,#0000ff
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.401, mean 3.98, maximum 5.096
Map values for surface "cap near": minimum 3.43, mean 3.797, maximum 4.966
> color electrostatic #4.1 map #3 palette
> 3.9,#0fc6ce:4.1,#6fdde1:4.3,#cff3f5:4.5,#ebd2de:51,#c4799e:5.3,#9e1f5e
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.406, mean 4.003, maximum 5.082
Map values for surface "cap near": minimum 3.428, mean 3.786, maximum 4.875
> color electrostatic #4.1 map #3 palette 3.9,#0fc6ce:4.1,#6fdde1:4.3,#cff3f5
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.392, mean 3.755, maximum 5.015
Map values for surface "cap near": minimum 3.511, mean 4.096, maximum 5.124
> color electrostatic #4.1 map #3 palette
> 3.9,#0000ff:4.1,#00ff00:4.3,#ff0000:4.5,#ebd2de:51,#c4799e:5.3,#9e1f5e
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.38, mean 3.859, maximum 4.992
Map values for surface "cap near": minimum 3.465, mean 3.979, maximum 5.122
> color electrostatic #4.1 map #3 palette
> 3.9,#0000ff:4.1,#00ccff:4.3,#00ff65:4.5,#66ff00:51,#ffcb00:5.3,#ff0000
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.38, mean 3.859, maximum 4.992
Map values for surface "cap near": minimum 3.465, mean 3.979, maximum 5.122
> color electrostatic #4.1 map #3 palette
> 3.7,#0000ff:4.1,#00ccff:4.3,#00ff65:4.5,#66ff00:51,#ffcb00:5.3,#ff0000
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.41, mean 4.012, maximum 5.072
Map values for surface "cap near": minimum 3.487, mean 3.864, maximum 5.103
> key blue:3.7 #00ccff:4.1 #00ff65:4.3 #66ff00:4.5 red:5.3 #ffcb00:51.0
> showTool true
> ui mousemode right "color key"
> color electrostatic #4.1 map #3 palette
> 3.7,#0000ff:4.1,#00ccff:4.3,#00ff65:4.5,#66ff00:5.1,#ffcb00:5.3,#ff0000
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.451, mean 3.963, maximum 5.047
> color electrostatic #4.1 map #3 palette
> 4.1,#0000ff:4.3,#00ccff:4.5,#00ff65:4.7,#66ff00:4.9,#ffcb00:5.1,#ff0000
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.473, mean 3.983, maximum 5.028
> color electrostatic #4.1 map #3 palette
> 3.7,#0000ff:3.9,#00ccff:4.2,#00ff65:4.5,#66ff00:4.8,#ffcb00:5.1,#ff0000
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap far": minimum 3.473, mean 3.983, maximum 5.028
> ui mousemode right translate
> key blue:3.7 #00ccff:3.9 #00ff65:4.2 #66ff00:4.5 #ffcb00:4.8 red:5.1
> showTool true
> ui mousemode right "color key"
> key pos 0.854978,0.521793 size 0.0378788,0.109589
> key pos 0.86039,0.613948 size 0,0
> key pos 0.86039,0.480697 size 0.0292208,0.13325
> key labelSide right/bottom
> key pos 0.861472,0.463263 size 0,0
> ui mousemode right translate
> ui mousemode right "color key"
> ui mousemode right translate
> ui mousemode middle 'color key'
> key pos 0.858225,0.429639 size 0.0151515,0.0585305
> key pos 0.873377,0.308842 size 0.0021645,0.119552
> ui mousemode middle translate
> ui mousemode right 'color key'
> key pos 0.788961,0.6401 size 0.00108225,0.00249066
> key pos 0.877706,0.429101 size 0.0313853,0.114921
> key pos 0.874459,0.419833 size 0.0422078,0.0824838
> key pos 0.84632,0.455051 size 0.0335498,0.0926784
> key pos 0.831169,0.638554 size 0,0
> key pos 0.920996,0.411492 size 0.0281385,0.175162
> key pos 0.852814,0.451344 size 0.0238095,0.162187
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/local_resolution/local_res_detail.cxs
> ui mousemode right translate
> ui mousemode right "color key"
> key pos 0.896104,0.513076 size 0.012987,0.0647572
> key pos 0.90368,0.405978 size 0.0357143,0.252802
> key pos 0.885281,0.506849 size 0.0714286,0.0199253
> key pos 0.378788,0.0523039 size 0.41342,0.00871731
> key pos 0.796537,0.0660025 size 0,0
[Repeated 2 time(s)]
> key pos 0.816017,0.104608 size 0,0
[Repeated 2 time(s)]
> key pos 0.745671,0.559153 size 0.0411255,0.0672478
> key pos 0.649351,0.348692 size 0.152597,0.011208
> key pos 0.835498,0.326276 size 0.109307,0.303861
> ui mousemode right translate
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Fig1/local_resolution/local_res_detail.cxs
——— End of log from Fri Mar 10 16:48:37 2023 ———
opened ChimeraX session
> ui tool show "Surface Color"
> key blue:3.7 #00ccff:3.9 #00ff65:4.2 #66ff00:4.5 #ffcb00:4.8 red:5.1
> showTool true
> ui mousemode right "color key"
> key pos 0.777056,0.283935 size 0.0108225,0.0859278
> key pos 0.724026,0.362391 size 0.0692641,0.198007
> key pos 0.75,0.195517 size 0.140693,0.407223
> key pos 0.367965,0.11208 size 0.358225,0.0136986
> key labelColor #bfbfbf
> key pos 0.356061,0.109589 size 0.304113,0.0161893
> key pos 0.880952,0.246575 size 0.0183983,0.328767
> key labelColor default
> key pos 0.874459,0.281445 size 0.00541126,0.372354
> key pos 0.878788,0.28269 size 0,0
> key greys-6 :3.7 :3.9 :4.2 :4.5 :4.8 :5.1
> color electrostatic #4.1 map #3 palette
> 3.7,#0000ff:3.9,#00ccff:4.2,#00ff65:4.5,#66ff00:4.8,#ffcb00:5.1,#ff0000
Map values for surface "surface": minimum 3.38, mean 3.986, maximum 5.34
Map values for surface "cap near": minimum 3.496, mean 3.716, maximum 4.698
Map values for surface "cap far": minimum 3.532, mean 4.008, maximum 5.047
> ui mousemode right translate
> ui tool show "Side View"
> save /home/mmartinezm/Desktop/image2.png supersample 3
> save /home/mmartinezm/Desktop/image3.png supersample 3
> key blue:3.7 #00ccff:3.9 #00ff65:4.2 #66ff00:4.5 #ffcb00:4.8 red:5.1
> showTool true
> ui mousemode right "color key"
> key pos 0.912338,0.389788 size 0.021645,0.211706
> key pos 0.867965,0.305106 size 0.00324675,0.201743
> key borderColor #bfbfbf
> key borderColor default
> key borderColor #bfbfbf
> key pos 0.849567,0.205479 size 0.0270563,0.161893
> key borderColor default
> ui mousemode right translate
> ui mousemode middle 'color key'
> key pos 0.784632,0.306351 size 0.0606061,0.277709
> key pos 0.807359,0.353674 size 0.0194805,0.0236613
> key pos 0.753247,0.425903 size 0.00757576,0.0261519
> ui mousemode middle translate
> ui mousemode right 'color key'
> key colorTreatment distinct
> key pos 0.794372,0.438356 size 0.0411255,0.0298879
> ui mousemode right translate
> key blue:3.7 #00ccff:3.9 #00ff65:4.2 #66ff00:4.5 #ffcb00:4.8 red:5.1
> showTool true
> ui mousemode right "color key"
> key pos 0.858225,0.288917 size 0.0324675,0.318804
> ui mousemode right translate
> ui mousemode right "color key"
> key pos 0.732684,0.348692 size 0.0573593,0.281445
> key pos 0.788961,0.347447 size 0,0
[Repeated 1 time(s)]
> ui mousemode right translate
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Supplementary_material/Asc1_TMs/local_res_TMs.cxs
——— End of log from Tue Mar 14 08:51:13 2023 ———
opened ChimeraX session
> show #5 models
> ui tool show "Surface Color"
> key blue:3.7 #00ccff:3.9 #00ff65:4.2 #66ff00:4.5 #ffcb00:4.8 red:5.1
> showTool true
> ui mousemode right "color key"
> key pos 0.800866,0.201743 size 0.0443723,0.308842
> key colorTreatment blended
> ui mousemode right translate
> save
> /home/mmartinezm/Documents/Manuscripts/2023_Asc1_Palacin/Figures/Supplementary_material/Asc1_TMs/local_res_TMs.cxs
——— End of log from Tue Mar 14 08:52:57 2023 ———
opened ChimeraX session
OpenGL version: 3.3.0 NVIDIA 535.104.05
OpenGL renderer: NVIDIA GeForce GTX 1080 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: en_US.UTF-8
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: HP
Model: HP Z4 G4 Workstation
OS: Ubuntu 22.04 Jammy Jellyfish
Architecture: 64bit ELF
Virtual Machine: none
CPU: 28 Intel(R) Xeon(R) W-2275 CPU @ 3.30GHz
Cache Size: 19712 KB
Memory:
total used free shared buff/cache available
Mem: 31Gi 2.5Gi 15Gi 55Mi 12Gi 28Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
15:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP102 [GeForce GTX 1080 Ti] [10de:1b06] (rev a1)
Subsystem: ASUSTeK Computer Inc. GP102 [GeForce GTX 1080 Ti] [1043:85e5]
Kernel driver in use: nvidia
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2023.5.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9.1
ChimeraX-AddH: 2.2.5
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.2
ChimeraX-BondRot: 2.0.1
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.1
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.4
ChimeraX-DockPrep: 1.1.1
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: 1.1.1
ChimeraX-Hbonds: 2.4
ChimeraX-Help: 1.2.1
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-Label: 1.1.7
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.2
ChimeraX-Map: 1.1.4
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: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.7
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7.2
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.1.1
ChimeraX-ShowSequences: 1.0.1
ChimeraX-SideView: 1.0.1
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.10.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.2
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.4
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.3
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.7
decorator: 5.1.1
distro: 1.7.0
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.3
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.6.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.6
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.7
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.1
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pexpect: 4.8.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.5.0
prompt-toolkit: 3.0.38
psutil: 5.9.4
ptyprocess: 0.7.0
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.3
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.3
python-dateutil: 2.8.2
pytz: 2023.3
pyzmq: 25.0.2
qtconsole: 5.4.0
QtPy: 2.3.1
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4.1
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.3.1
traitlets: 5.9.0
typing-extensions: 4.5.0
tzdata: 2023.3
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.7
zipp: 3.15.0
Change History (2)
comment:1 by , 2 years ago
| Component: | Unassigned → Sessions |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → restore_snapshot for "Volume" returned None |
comment:2 by , 2 years ago
| Resolution: | → fixed |
|---|---|
| Status: | assigned → closed |
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Fixed.
User restored a session and a volume file was missing and they did not replace it. That volume was being used to color a surface and so the surface coloring failed with a traceback. I fixed the code so the surface coloring just gives a warning message that the coloring was not restored. There was already code to give that warning from 5 years ago but it did the wrong test so it didn't work.