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Opened 8 months ago
Closed 8 months ago
#17116 closed defect (duplicate)
MemoryError saving map in session
| Reported by: | Owned by: | Greg Couch | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Sessions | Version: | |
| Keywords: | Cc: | Tom Goddard | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.19045
ChimeraX Version: 1.4 (2022-06-03 23:39:42 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.4 (2022-06-03)
© 2016-2022 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open E:/LILab/20241218MtbRPo/cryosparc_P58_J40_003_volume_map.mrc
Opened cryosparc_P58_J40_003_volume_map.mrc as #1, grid size 640,640,640,
pixel 0.445, shown at level 0.0112, step 4, values float32
> open E:/LILab/20241218MtbRPo/RealSpaceRefine_8/MtbRPo_sigJ-
> coot-23_real_space_refined.pdb
Chain information for MtbRPo_sigJ-coot-23_real_space_refined.pdb #2
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
I | No description available
> hide atoms
> show cartoons
> hide #!1 models
> select /G
943 atoms, 1058 bonds, 46 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 943 atom styles
> select #2/H
932 atoms, 1041 bonds, 46 residues, 1 model selected
> style sel stick
Changed 932 atom styles
> hide sel cartoons
> show sel atoms
> volume all level 0.01
> volume #1 step 1
> select #2/H:2-6
101 atoms, 112 bonds, 5 residues, 1 model selected
> select #2/A
1687 atoms, 1712 bonds, 222 residues, 1 model selected
> color sel palegreen goldnrod
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> color sel pale goldenrod
> select #2/B
1800 atoms, 1827 bonds, 237 residues, 1 model selected
> color sel mistyrose
> select #2/C
8690 atoms, 8849 bonds, 1122 residues, 1 model selected
> color sel light gray
> select #2/D
10019 atoms, 10190 bonds, 1281 residues, 1 model selected
> color sel gray
> select #2/H:2-6
101 atoms, 112 bonds, 5 residues, 1 model selected
> color sel red
> select #2/H:1
21 atoms, 22 bonds, 1 residue, 1 model selected
> set bgColor white
> set bgColor #ffffff00
> lighting soft
> color sel orange
> select #2/H:7-25
392 atoms, 438 bonds, 19 residues, 1 model selected
> color sel orange
> select #2/H:26-37
235 atoms, 261 bonds, 12 residues, 1 model selected
> select #2/H:26-31
120 atoms, 132 bonds, 6 residues, 1 model selected
> color sel red
> select #2/H:32-46
298 atoms, 333 bonds, 15 residues, 1 model selected
> color sel orange
> select clear
> ui tool show "Color Actions"
> lighting flat
> lighting shadows true intensity 0.5
> lighting shadows false
> lighting shadows true
> lighting shadows false
> lighting shadows true
> lighting flat
> dssp
> select #2/G:48
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel orange
> select #2/B
1800 atoms, 1827 bonds, 237 residues, 1 model selected
> color sel mistyrose
> select clear
> select #2/B
1800 atoms, 1827 bonds, 237 residues, 1 model selected
> ui tool show "Color Actions"
[Repeated 1 time(s)]
> color sel misty rose
[Repeated 6 time(s)]
> color sel bisque
> color sel chartreuse
> color sel misty rose
> color sel pale goldenrod
> color sel hot pink
> color sel seashell
[Repeated 1 time(s)]
> color sel misty rose
> color sel pink
> color sel peach puff
> color sel pink
> select clear
> select #2/G:43-47
104 atoms, 116 bonds, 5 residues, 1 model selected
> select #2/G:42-47
124 atoms, 138 bonds, 6 residues, 1 model selected
> color sel red
> select #2/H:26-37
235 atoms, 261 bonds, 12 residues, 1 model selected
> select #2/H:2-8
142 atoms, 158 bonds, 7 residues, 1 model selected
> color sel red
> select #2/H:7-25
392 atoms, 438 bonds, 19 residues, 1 model selected
> color sel orange
> select #2/H:2-7
122 atoms, 136 bonds, 6 residues, 1 model selected
> color sel red
> select #2/G:24-41
367 atoms, 412 bonds, 18 residues, 1 model selected
> color sel orange
> select #2/G:3-11
186 atoms, 208 bonds, 9 residues, 1 model selected
> color sel orange
> select #2/G:12-23
245 atoms, 273 bonds, 12 residues, 1 model selected
> color sel forest green
> select #2/I
106 atoms, 117 bonds, 5 residues, 1 model selected
> ui tool show "Color Actions"
> color sel blue violet
> show sel atoms
> hide sel cartoons
> color sel purple
> select #2/H:26-37
235 atoms, 261 bonds, 12 residues, 1 model selected
> color sel orange
> select #2/H:24-29
119 atoms, 131 bonds, 6 residues, 1 model selected
> color sel red
> select #2/G:24-25
41 atoms, 45 bonds, 2 residues, 1 model selected
> color sel red
> select clear
> select #2/F:1-71
562 atoms, 573 bonds, 70 residues, 1 model selected
> color sel yellow
> select #2/F:72-91
143 atoms, 147 bonds, 20 residues, 1 model selected
> color sel lime
> select #2/F:92-158
498 atoms, 505 bonds, 67 residues, 1 model selected
> color sel royal blue
> select #2/F:159-312
281 atoms, 286 bonds, 40 residues, 1 model selected
> color sel magenta
> select clear
> select #2/A
1687 atoms, 1712 bonds, 222 residues, 1 model selected
> color sel dark gray
> select #2/B
1800 atoms, 1827 bonds, 237 residues, 1 model selected
> color sel dark gray
> select #2/C
8690 atoms, 8849 bonds, 1122 residues, 1 model selected
> color sel dark gray
> select #2/D
10019 atoms, 10190 bonds, 1281 residues, 1 model selected
> color sel dark gray
> select #2/E
659 atoms, 672 bonds, 84 residues, 1 model selected
> color sel dark gray
> lighting soft
> preset cartoons/nucleotides cylinders/stubs
Using preset: Cartoons/Nucleotides / Cylinders/Stubs
Changed 24338 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
cartoon style protein modeh tube rad 2 sides 24 thick 0.6
cartoon style nucleic x round width 1.6 thick 1.6
nucleotides stubs
> preset cartoons/nucleotides ribbons/slabs
Using preset: Cartoons/Nucleotides / Ribbons/Slabs
Changed 0 atom styles
Preset expands to these ChimeraX commands:
show nucleic
hide protein|solvent|H
surf hide
style (protein|nucleic|solvent) & @@draw_mode=0 stick
cartoon
cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
cartoon style ~(nucleic|strand) x round
cartoon style (nucleic|strand) x rect
nucleotides tube/slab shape box
> ui tool show "Side View"
> ui tool show "Color Actions"
> color sel LIGHT gray
Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero',
'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', or 'random'
or a keyword
> color sel light gray
> select #2/C
8690 atoms, 8849 bonds, 1122 residues, 1 model selected
> color sel light gray
> select #2/D
10019 atoms, 10190 bonds, 1281 residues, 1 model selected
> color sel light gray
> select #2/C
8690 atoms, 8849 bonds, 1122 residues, 1 model selected
> color sel light gray
> select #2/A
1687 atoms, 1712 bonds, 222 residues, 1 model selected
> color sel light gray
> select #2/B
1800 atoms, 1827 bonds, 237 residues, 1 model selected
> color sel light gray
> select #2/D
10019 atoms, 10190 bonds, 1281 residues, 1 model selected
> color sel light gray
> select #2/D
10019 atoms, 10190 bonds, 1281 residues, 1 model selected
> color sel light gray
> select #2/E
659 atoms, 672 bonds, 84 residues, 1 model selected
> color sel light gray
> select clear
> select #2/E
659 atoms, 672 bonds, 84 residues, 1 model selected
> color sel light gray
> select #2/D
10019 atoms, 10190 bonds, 1281 residues, 1 model selected
> color sel light gray
> select #2/C
8690 atoms, 8849 bonds, 1122 residues, 1 model selected
> color sel light gray
> select clear
> select #2/G
943 atoms, 1058 bonds, 46 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> select #2/H
932 atoms, 1041 bonds, 46 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 932 atom styles
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
[Repeated 1 time(s)]
> show sel cartoons
> hide sel cartoons
> style sel stick
Changed 932 atom styles
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> style sel sphere
Changed 932 atom styles
> style sel stick
Changed 932 atom styles
> show sel atoms
> hide sel cartoons
> nucleotides sel atoms
> style nucleic & sel stick
Changed 932 atom styles
> select #2/G
943 atoms, 1058 bonds, 46 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 943 atom styles
> select #2/I
106 atoms, 117 bonds, 5 residues, 1 model selected
> nucleotides sel atoms
> style nucleic & sel stick
Changed 106 atom styles
> show sel atoms
> hide sel atoms
[Repeated 1 time(s)]
> show sel atoms
> hide sel cartoons
> ui tool show "Side View"
> select clear
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting soft
> lighting simple
> lighting soft
> lighting flat
> lighting full
> lighting simple
> graphics silhouettes false
> lighting shadows true
> lighting flat
> lighting full
> lighting soft
> lighting simple
> lighting soft
> graphics silhouettes false
> graphics silhouettes true
> lighting flat
[Repeated 1 time(s)]
> lighting soft
> lighting flat
[Repeated 3 time(s)]
> lighting soft
> lighting flat
> lighting soft
> lighting flat
> ui tool show "Color Actions"
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> lighting soft
[Repeated 1 time(s)]
> lighting shadows true intensity 0.5
> lighting flat
> show #!1 models
> select add #1
3 models selected
> select subtract #1
Nothing selected
> select add #1
3 models selected
> transparency #1.1 50
> surface #1.1
No atoms specified by #1.1
> select subtract #1
Nothing selected
> hide #!1 models
> lighting soft
> select #2/F:1-71
562 atoms, 573 bonds, 70 residues, 1 model selected
> color sel yellow
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> select #2/C
8690 atoms, 8849 bonds, 1122 residues, 1 model selected
> select clear
> volume zone #1 nearAtoms #2/H:1 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #3, grid size 640,640,640,
pixel 0.445, shown at step 1, values float32
> select add #3
2 models selected
> transparency #3.1 50
> volume zone #1 nearAtoms #2/H:2-7 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #4, grid size 640,640,640,
pixel 0.445, shown at step 1, values float32
> select add #4
4 models selected
> select subtract #3
2 models selected
> transparency #4.1 50
> ui tool show "Color Actions"
> color #4 lavender
[Repeated 1 time(s)]
> select subtract #4
Nothing selected
> color #4 plum
> color #4 pink
> hide #!4 models
> show #!4 models
> color #4 thistle
> color #4 pink
> hide #!4 models
> show #!4 models
> volume zone #1 nearAtoms #2/H:8-23 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #5, grid size 640,640,640,
pixel 0.445, shown at step 1, values float32
> select add #5
2 models selected
> transparency #5.1 50
> color sel yellow
> hide #!5 models
> show #!5 models
> color sel khaki
> color #5 #ffff7f models transparency 0
> transparency #5.1 50
> color sel light goldenrod yellow
> color sel pale goldenrod
> color #5 #fdff6a models transparency 0
> color #5 #fffb82 models transparency 0
> color #5 #fffc9e models transparency 0
> color #5 #ffffb4 models transparency 0
> color #5 #ffffc0 models transparency 0
> color #5 #ffffb7 models transparency 0
> color #5 #fffabb models transparency 0
> color #5 #ffffbb models transparency 0
> transparency #5.1 50
> volume zone #1 nearAtoms #2/H:24-29 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #6, grid size 640,640,640,
pixel 0.445, shown at step 1, values float32
> color #6 pink
> select add #6
4 models selected
> select subtract #5
2 models selected
> transparency #6.1 50
> volume zone #1 nearAtoms #2/H:30-46 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #7, grid size 640,640,640,
pixel 0.445, shown at step 1, values float32
> select subtract #6
Nothing selected
> select add #7
2 models selected
> transparency #7.1 50
> ui tool show "Color Actions"
> color sel gold
> color sel lemon chiffon
> color sel moccasin
> color sel gold
> color sel antique white
> color sel light goldenrod yellow
> color sel old lace
> color sel wheat
> color sel khaki
> color sel pale goldenrod
> color sel khaki
> hide #!7 models
> show #!7 models
> color sel sandy brown
[Repeated 1 time(s)]
> color sel gold
> color sel dark orange
> color sel orange
> hide #!7 models
> show #!7 models
> color #5 dark orange
> color #3 dark orange
> color #4 red
> ui tool show "Color Actions"
> color #4 orange red
> color #6 orange red
> volume zone #1 nearAtoms #2/G:48 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #8, grid size 640,640,640,
pixel 0.445, shown at step 1, values float32
> select subtract #7
Nothing selected
> select add #8
2 models selected
> transparency #8.1 50
> color #8 dark orange
> hide #!8 models
> show #!8 models
> select subtract #8
Nothing selected
> volume zone #1 nearAtoms #2/G:42-47 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #9, grid size 640,640,640,
pixel 0.445, shown at step 1, values float32
> color #9 orange red
> select add #9
2 models selected
> transparency #9.1 50
> volume zone #1 nearAtoms #2/G:26-41 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #10, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> select subtract #9
Nothing selected
> select add #10
2 models selected
> transparency #10.1 50
> color #10 dark orange
> volume zone #1 nearAtoms #2/G:24-25 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #11, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> select subtract #10
Nothing selected
> select add #11
2 models selected
> transparency #11.1 50
> color #11 orange red
> volume zone #1 nearAtoms #2/G:12-23 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #12, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> color #12 lime
> select subtract #11
Nothing selected
> select add #12
2 models selected
> transparency #12.1 50
> volume zone #1 nearAtoms #2/G:3-11 range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #13, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> select subtract #12
Nothing selected
> select add #13
2 models selected
> transparency #13.1 50
> color #13 dark orange
> volume zone #1 nearAtoms #2/I range 1 newMap true
Opened cryosparc_P58_J40_003_volume_map.mrc zone as #14, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> select subtract #13
Nothing selected
> select add #14
2 models selected
> transparency #14.1 50
> ui tool show "Color Actions"
> color #14 violet
> color #14 pink
> color #14 violet
> select clear
> ui tool show "Color Actions"
> color #12 pale green
> ui tool show "Color Actions"
> color #3 wheat
> select add #13
2 models selected
> select subtract #13
Nothing selected
> select add #13
2 models selected
> color #13 dark orange
> select subtract #13
Nothing selected
> select #2/F:72-91
143 atoms, 147 bonds, 20 residues, 1 model selected
> color sel blue
> select #2/F:92-158
498 atoms, 505 bonds, 67 residues, 1 model selected
> color sel lime
> select clear
> ui tool show "Color Actions"
> hide #!14 models
> show #!14 models
> color #14 orchid
> color #14 dark orchid
> select add #14
2 models selected
> transparency #14.1 70
> select subtract #14
Nothing selected
> select add #13
2 models selected
> transparency #13.1 70
> select add #12
4 models selected
> select subtract #13
2 models selected
> transparency #12.1 70
> select subtract #12
Nothing selected
> select add #11
2 models selected
> transparency #11.1 70
> select subtract #11
Nothing selected
> select add #10
2 models selected
> transparency #10.1 70
> select subtract #10
Nothing selected
> select add #9
3 models selected
> transparency #9.1 70
> select subtract #9
Nothing selected
> select add #8
3 models selected
> transparency #8.1 70
> select subtract #8
Nothing selected
> select add #7
2 models selected
> transparency #7.1 70
> select subtract #7
Nothing selected
> select add #7
2 models selected
> select subtract #7
Nothing selected
> select add #7
2 models selected
> select add #4
4 models selected
> select subtract #7
2 models selected
> select add #3
5 models selected
> select add #5
7 models selected
> select add #6
9 models selected
> select add #7
11 models selected
> select add #8
14 models selected
> select add #9
17 models selected
> select add #10
19 models selected
> select add #11
21 models selected
> select add #12
23 models selected
> select add #13
25 models selected
> select add #14
27 models selected
> transparency #3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1 70
> select add #2
26320 atoms, 26980 bonds, 3240 residues, 28 models selected
> select add #1
26320 atoms, 26980 bonds, 3240 residues, 30 models selected
> select subtract #2
29 models selected
> transparency #3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1 70
> select subtract #1
27 models selected
> select add #4
28 models selected
> select add #5
29 models selected
> select add #10
30 models selected
> transparency #3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1 70
> unsel all
Unknown command: unsel all
> unselect all
Unknown command: unselect all
> select subtract #14
28 models selected
> select subtract #13
26 models selected
> select subtract #12
24 models selected
> select subtract #11
22 models selected
> select subtract #10
19 models selected
> select subtract #9
16 models selected
> select subtract #8
13 models selected
> select subtract #7
11 models selected
> select subtract #6
9 models selected
> select subtract #5
6 models selected
> select subtract #4
3 models selected
> select subtract #3
Nothing selected
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #3
3 models selected
> transparency #3.1 70
> select subtract #3
Nothing selected
> select add #4
3 models selected
> transparency #4.1 70
> select add #5
6 models selected
> transparency #4.1#5.1 50
> transparency #4.1#5.1 70
> select subtract #5
3 models selected
> select subtract #4
Nothing selected
> select add #3
3 models selected
> select add #4
6 models selected
> select add #5
9 models selected
> select add #6
11 models selected
> select add #7
13 models selected
> select add #8
16 models selected
> select add #9
19 models selected
> select add #10
22 models selected
> select add #11
24 models selected
> select add #12
26 models selected
> select add #13
28 models selected
> select add #14
30 models selected
> transparency #3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1 80
> transparency #3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1 60
> transparency #3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1 70
> save E:/LILab/课题paper书写/figure/figure2.cxs
[Repeated 1 time(s)]
> view name fig2_1
> save Fig2b_1.tiff width 2000 height 2000 transparentBackground true
> transparency #3.1#4.1#5.1#6.1#7.1#8.1#9.1#10.1#11.1#12.1#13.1#14.1 50
> save Fig2b_1.tiff width 2000 height 2000 transparentBackground true
> select subtract #14
28 models selected
> select add #14
30 models selected
> select subtract #14
28 models selected
> select subtract #13
26 models selected
> select subtract #12
24 models selected
> select subtract #11
22 models selected
> select subtract #10
19 models selected
> select subtract #9
16 models selected
> select subtract #8
13 models selected
> select subtract #7
11 models selected
> select subtract #6
9 models selected
> select subtract #5
6 models selected
> select subtract #4
3 models selected
> select subtract #3
Nothing selected
> save Fig2b_1.tiff width 2000 height 2000 transparentBackground true
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #14
2 models selected
> select subtract #14
Nothing selected
> select add #14
2 models selected
> select clear
> color #3 #ffaa0080 models
> ui tool show "Color Actions"
> color #3 gold
> undo
[Repeated 1 time(s)]
> color #3 yellow
> color #3 orange
> select add #14
2 models selected
> select add #13
4 models selected
> select subtract #13
2 models selected
> select subtract #14
Nothing selected
> turn x 90
> ui tool show "Side View"
> view fig2_1
> turn x 90
> save Fig2b_2.tiff width 2000 height 2000 transparentBackground true
> select #2/G,H,I
1981 atoms, 2216 bonds, 97 residues, 1 model selected
> select ~sel
24339 atoms, 24764 bonds, 3143 residues, 39 models selected
> hide sel cartoons
> view fig2_1
> select subtract #1
24339 atoms, 24764 bonds, 3143 residues, 37 models selected
> select add #2
26320 atoms, 26980 bonds, 3240 residues, 37 models selected
> select subtract #3
26320 atoms, 26980 bonds, 3240 residues, 34 models selected
> select subtract #2
33 models selected
> select subtract #4
30 models selected
> select subtract #5
27 models selected
> select subtract #6
24 models selected
> select subtract #7
21 models selected
> select subtract #8
18 models selected
> select subtract #9
15 models selected
> select subtract #10
12 models selected
> select subtract #11
9 models selected
> select subtract #12
6 models selected
> select subtract #13
3 models selected
> select subtract #14
Nothing selected
> select add #14
3 models selected
> select subtract #14
Nothing selected
> save Fig2b_3.tiff width 2000 height 2000 transparentBackground true
> select ~sel
26320 atoms, 26980 bonds, 3240 residues, 39 models selected
> show sel cartoons
> hide sel cartoons
> select ~sel
Nothing selected
> show cartoons
> show atoms
> undo
> select #2/G,H,I
1981 atoms, 2216 bonds, 97 residues, 1 model selected
> hide sel cartoons
> select add #2
26320 atoms, 26980 bonds, 3240 residues, 1 model selected
> select subtract #2
Nothing selected
> lighting soft
[Repeated 1 time(s)]
> lighting flat
> lighting soft
> lighting flat
> open E:/LILab/20241112MtbRPo/cryosparc_P57_J282_003_volume_map.mrc
Opened cryosparc_P57_J282_003_volume_map.mrc as #15, grid size 640,640,640,
pixel 0.445, shown at level 0.0124, step 4, values float32
> hide #!14 models
> hide #!13 models
> hide #!12 models
> hide #!11 models
> hide #!10 models
> hide #!9 models
> hide #!8 models
> hide #!7 models
> hide #!6 models
> hide #!5 models
> hide #!4 models
> hide #!3 models
> hide #2 models
> lighting soft
> lighting flat
> lighting soft
> lighting shadows true intensity 0.5
> lighting flat
> lighting soft
> open E:/LILab/20241112MtbRPo/RealSpaceRefine_4/close_bubble_MtbRPo-
> coot-0_real_space_refined_real_space_refined.pdb
Chain information for close_bubble_MtbRPo-
coot-0_real_space_refined_real_space_refined.pdb #16
---
Chain | Description
A | No description available
B | No description available
C | No description available
D | No description available
E | No description available
F | No description available
G | No description available
H | No description available
> hide #16 atoms
> show #16 cartoons
> select add #15
3 models selected
> transparency #15.1 50
> volume #15 level 0.005
> volume #15 level 0.008
> hide #!15 models
> select subtract #15
Nothing selected
> select #16/A
1687 atoms, 1712 bonds, 222 residues, 1 model selected
> color sel light gray
> select #16/B
1800 atoms, 1827 bonds, 237 residues, 1 model selected
> color sel light gray
> select #16/C
8690 atoms, 8849 bonds, 1122 residues, 1 model selected
> color sel light gray
> select #16/D
10019 atoms, 10190 bonds, 1281 residues, 1 model selected
> color sel light gray
> select #16/E
659 atoms, 672 bonds, 84 residues, 1 model selected
> color sel light gray
> dssp
> select #16/F:1-71
562 atoms, 573 bonds, 70 residues, 1 model selected
> color sel light yellow
> color sel yellow
> color #3 light yellow
> show #!3 models
> select add #3
562 atoms, 573 bonds, 70 residues, 3 models selected
> show #2 models
> hide #!3 models
> hide #2 models
> show #2 models
> show #!3 models
> show #!1 models
> hide #!1 models
> select subtract #3
562 atoms, 573 bonds, 70 residues, 1 model selected
> show #!5 models
> color #3 lightblue orange
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> hide #!3 models
> show #!3 models
> select add #3
562 atoms, 573 bonds, 70 residues, 3 models selected
> select subtract #3
562 atoms, 573 bonds, 70 residues, 1 model selected
> color #3 lightblue orange
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> hide #!3 models
> show #!3 models
> hide #!3 models
> show #!3 models
> color #5 lightblue orange
Expected a collection of one of 'All', 'atoms', 'bonds', 'cartoons', 'labels',
'models', 'pseudobonds', 'ribbons', 'rings', or 'surfaces' or a keyword
> hide #!5 models
> show #!5 models
> hide #!3 models
> show #!3 models
> ui tool show "Color Actions"
> color #5 wheat
> hide #!5 models
> show #!5 models
> color #3 wheat
> hide #!3 models
> show #!3 models
> show #!7 models
> hide #!7 models
> show #!10 models
> hide #!10 models
> show #!10 models
> hide #!10 models
> hide #!5 models
> hide #!3 models
> hide #2 models
> save E:/LILab/课题paper书写/figure/figure2.cxs
> select #16/F:72-91
143 atoms, 147 bonds, 20 residues, 1 model selected
> color sel blue
> select #16/F:92-158
498 atoms, 505 bonds, 67 residues, 1 model selected
> color sel lime
> select #16/F:159-312
281 atoms, 286 bonds, 40 residues, 1 model selected
> color sel magenta
> select #16/H:1
21 atoms, 22 bonds, 1 residue, 1 model selected
> select #16/H
932 atoms, 1041 bonds, 46 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 932 atom styles
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 932 atom styles
> select #16/G
943 atoms, 1058 bonds, 46 residues, 1 model selected
> show sel atoms
> hide sel cartoons
> style sel stick
Changed 943 atom styles
> select #16/H:1
21 atoms, 22 bonds, 1 residue, 1 model selected
> color sel orange
> select #16/H:2-7
122 atoms, 136 bonds, 6 residues, 1 model selected
> color sel red
> select #16/H:8-23
330 atoms, 368 bonds, 16 residues, 1 model selected
> color sel orange
> select #16/H:24-29
119 atoms, 131 bonds, 6 residues, 1 model selected
> color sel red
> select #16/H:30-46
340 atoms, 380 bonds, 17 residues, 1 model selected
> color sel orange
> select #16/G:48
21 atoms, 23 bonds, 1 residue, 1 model selected
> color sel orange
> select #16/G:42-47
124 atoms, 138 bonds, 6 residues, 1 model selected
> color sel red
> select #16/G:26-41
326 atoms, 366 bonds, 16 residues, 1 model selected
> color sel orange
> select #16/G:24-25
41 atoms, 45 bonds, 2 residues, 1 model selected
> color sel red
> select #16/G:12-23
245 atoms, 273 bonds, 12 residues, 1 model selected
> color sel forest green
> select #16/G:3-11
186 atoms, 208 bonds, 9 residues, 1 model selected
> color sel orange
> select #16/F:72-91
143 atoms, 147 bonds, 20 residues, 1 model selected
> color sel green
> select #16/F:92-158
498 atoms, 505 bonds, 67 residues, 1 model selected
> color sel blue
> select #16/F:72-91
143 atoms, 147 bonds, 20 residues, 1 model selected
> color sel lime
> volume zone #15 nearAtoms #16/H:1 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #17, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> select add #17
143 atoms, 147 bonds, 20 residues, 3 models selected
> select add #16
26214 atoms, 26863 bonds, 3235 residues, 3 models selected
> select subtract #16
2 models selected
> transparency #17.1 70
> volume zone #15 nearAtoms #16/H:2-7 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #18, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> select subtract #17
Nothing selected
> select add #18
2 models selected
> transparency #18.1 70
> volume zone #15 nearAtoms #16/H:8-23 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #19, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> volume zone #15 nearAtoms #16/H:24-29 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #20, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> volume zone #15 nearAtoms #16/H:30-46 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #21, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> volume zone #15 nearAtoms #16/G:48 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #22, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> volume zone #15 nearAtoms #16/G:42-47 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #23, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> volume zone #15 nearAtoms #16/G:26-41 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #24, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> volume zone #15 nearAtoms #16/G:24-25 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #25, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> volume zone #15 nearAtoms #16/G:12-23 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #26, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> volume zone #15 nearAtoms #16/G:3-11 range 2 newMap true
Opened cryosparc_P57_J282_003_volume_map.mrc zone as #27, grid size
640,640,640, pixel 0.445, shown at step 1, values float32
> select add #17
4 models selected
> select add #19
6 models selected
> select add #20
8 models selected
> select add #21
10 models selected
> select add #22
12 models selected
> select add #23
14 models selected
> select add #24
16 models selected
> select add #25
18 models selected
> select add #26
20 models selected
> select add #27
22 models selected
> transparency #17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1 50
> transparency #17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1 70
> transparency #17.1#18.1#19.1#20.1#21.1#22.1#23.1#24.1#25.1#26.1#27.1 50
> save E:/LILab/课题paper书写/figure/figure2.cxs
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
> save E:/LILab/课题paper书写/figure/figure2.cxs
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\session.py", line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x00000123595CEEB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000123222E5910> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000123222E5520>
'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x00000123248FC5B0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x00000123595CEEB0> -> <chimerax.map.volume.VolumeSurface object at
0x00000123222E5910> 'surface' -> <chimerax.map.volume.Volume object at
0x00000123222E5520> 'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x00000123248FC5B0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000123595CEEB0> -> <chimerax.map.volume.VolumeSurface object at
0x00000123222E5910> 'surface' -> <chimerax.map.volume.Volume object at
0x00000123222E5520> 'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x00000123248FC5B0>
ValueError: error processing: 'models' -> -> 'surface' ->
'cryosparc_P57_J282_003_volume_map.mrc zone' -> : Error while saving session
data for 'models' -> -> 'surface' -> 'cryosparc_P57_J282_003_volume_map.mrc
zone' ->
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\session.py", line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x00000123595CEEB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000123222E5910> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000123222E5520>
'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x00000123248FC5B0>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x00000123595CEEB0> -> <chimerax.map.volume.VolumeSurface object at
0x00000123222E5910> 'surface' -> <chimerax.map.volume.Volume object at
0x00000123222E5520> 'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x00000123248FC5B0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000123595CEEB0> -> <chimerax.map.volume.VolumeSurface object at
0x00000123222E5910> 'surface' -> <chimerax.map.volume.Volume object at
0x00000123222E5520> 'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x00000123248FC5B0>
ValueError: error processing: 'models' -> -> 'surface' ->
'cryosparc_P57_J282_003_volume_map.mrc zone' -> : Error while saving session
data for 'models' -> -> 'surface' -> 'cryosparc_P57_J282_003_volume_map.mrc
zone' ->
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
> save E:/figure2.cxs
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 630, in save
fserialize(stream, data)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\serialize.py", line 65, in msgpack_serialize
stream.write(packer.pack(obj))
File "msgpack\\_packer.pyx", line 294, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 300, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 297, in msgpack._cmsgpack.Packer.pack
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
MemoryError
MemoryError
File "msgpack\\_packer.pyx", line 231, in msgpack._cmsgpack.Packer._pack
See log for complete Python traceback.
> save E:/figure2.cxs
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\session.py", line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x00000123595CEEB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000123222E5910> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000123222E5520>
'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x0000012356D51640>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x00000123595CEEB0> -> <chimerax.map.volume.VolumeSurface object at
0x00000123222E5910> 'surface' -> <chimerax.map.volume.Volume object at
0x00000123222E5520> 'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x0000012356D51640>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000123595CEEB0> -> <chimerax.map.volume.VolumeSurface object at
0x00000123222E5910> 'surface' -> <chimerax.map.volume.Volume object at
0x00000123222E5520> 'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x0000012356D51640>
ValueError: error processing: 'models' -> -> 'surface' ->
'cryosparc_P57_J282_003_volume_map.mrc zone' -> : Error while saving session
data for 'models' -> -> 'surface' -> 'cryosparc_P57_J282_003_volume_map.mrc
zone' ->
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process
data = sm.take_snapshot(obj, session, self.state_flags)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\session.py", line 200, in take_snapshot
data = state_from_grid_data(self.grid_data, session_path =
session.session_file_path,
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\map\session.py", line 310, in state_from_grid_data
bytes = dt.matrix().tobytes()
MemoryError
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery
self.processed[key] = self.process(obj, parents)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 290, in process
raise RuntimeError(msg) from e
RuntimeError: Error while saving session data for 'models' ->
<chimerax.core.models.Models object at 0x00000123595CEEB0> ->
<chimerax.map.volume.VolumeSurface object at 0x00000123222E5910> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000123222E5520>
'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x0000012356D51640>
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog
_dlg.display(session, **kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display
run(session, cmd)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run
results = command.run(text, log=log, return_json=return_json)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save
Command(session, registry=registry).run(provider_cmd_text, log=log)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run
result = ci.function(session, **kw_args)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save
saver_info.save(session, path, **provider_kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save
return cxs_save(session, path, **kw)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 896, in save
session.save(output, version=version, include_maps=include_maps)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save
mgr.discovery(self._state_containers)
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
ValueError: error processing: 'models' -> <chimerax.core.models.Models object
at 0x00000123595CEEB0> -> <chimerax.map.volume.VolumeSurface object at
0x00000123222E5910> 'surface' -> <chimerax.map.volume.Volume object at
0x00000123222E5520> 'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x0000012356D51640>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000123595CEEB0> -> <chimerax.map.volume.VolumeSurface object at
0x00000123222E5910> 'surface' -> <chimerax.map.volume.Volume object at
0x00000123222E5520> 'cryosparc_P57_J282_003_volume_map.mrc zone' ->
<chimerax.map.session.GridDataState object at 0x0000012356D51640>
ValueError: error processing: 'models' -> -> 'surface' ->
'cryosparc_P57_J282_003_volume_map.mrc zone' -> : Error while saving session
data for 'models' -> -> 'surface' -> 'cryosparc_P57_J282_003_volume_map.mrc
zone' ->
File "G:\ChimeraX-1.4\ChimeraX 1.4\bin\lib\site-
packages\chimerax\core\session.py", line 266, in discovery
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 556.39
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.0, Qt 6.3.0
Qt runtime version: 6.3.0
Qt platform: windows
Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 10 专业版 (Build 19045)
Memory: 34,206,019,584
MaxProcessMemory: 137,438,953,344
CPU: 16 Intel(R) Core(TM) i7-10700F CPU @ 2.90GHz
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.12
appdirs: 1.4.4
Babel: 2.10.1
backcall: 0.2.0
blockdiag: 3.0.0
certifi: 2022.5.18.1
cftime: 1.6.0
charset-normalizer: 2.0.12
ChimeraX-AddCharge: 1.2.3
ChimeraX-AddH: 2.1.11
ChimeraX-AlignmentAlgorithms: 2.0
ChimeraX-AlignmentHdrs: 3.2.1
ChimeraX-AlignmentMatrices: 2.0
ChimeraX-Alignments: 2.4.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.0
ChimeraX-Atomic: 1.39.1
ChimeraX-AtomicLibrary: 7.0
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.1
ChimeraX-BasicActions: 1.1
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 2.1.1
ChimeraX-BondRot: 2.0
ChimeraX-BugReporter: 1.0
ChimeraX-BuildStructure: 2.7
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.1
ChimeraX-ButtonPanel: 1.0
ChimeraX-CageBuilder: 1.0
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.2
ChimeraX-ChemGroup: 2.0
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.1
ChimeraX-CommandLine: 1.2.3
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0
ChimeraX-Core: 1.4
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.3.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0
ChimeraX-DataFormats: 1.2.2
ChimeraX-Dicom: 1.1
ChimeraX-DistMonitor: 1.1.5
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ExperimentalCommands: 1.0
ChimeraX-FileHistory: 1.0
ChimeraX-FunctionKey: 1.0
ChimeraX-Geometry: 1.2
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1
ChimeraX-Hbonds: 2.1.2
ChimeraX-Help: 1.2
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.1
ChimeraX-ItemsInspection: 1.0
ChimeraX-Label: 1.1.1
ChimeraX-ListInfo: 1.1.1
ChimeraX-Log: 1.1.5
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.8.1
ChimeraX-Map: 1.1
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0
ChimeraX-MapFilter: 2.0
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1
ChimeraX-Markers: 1.0
ChimeraX-Mask: 1.0
ChimeraX-MatchMaker: 2.0.6
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.1
ChimeraX-Meeting: 1.0
ChimeraX-MLP: 1.1
ChimeraX-mmCIF: 2.7
ChimeraX-MMTF: 2.1
ChimeraX-Modeller: 1.5.5
ChimeraX-ModelPanel: 1.3.2
ChimeraX-ModelSeries: 1.0
ChimeraX-Mol2: 2.0
ChimeraX-Morph: 1.0
ChimeraX-MouseModes: 1.1
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nucleotides: 2.0.2
ChimeraX-OpenCommand: 1.9
ChimeraX-PDB: 2.6.6
ChimeraX-PDBBio: 1.0
ChimeraX-PDBLibrary: 1.0.2
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1
ChimeraX-PubChem: 2.1
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1
ChimeraX-RemoteControl: 1.0
ChimeraX-ResidueFit: 1.0
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 2.0.1
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.6
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0
ChimeraX-Shortcuts: 1.1
ChimeraX-ShowAttr: 1.0
ChimeraX-ShowSequences: 1.0
ChimeraX-SideView: 1.0
ChimeraX-Smiles: 2.1
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.8
ChimeraX-STL: 1.0
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.0.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0
ChimeraX-SwapAA: 2.0
ChimeraX-SwapRes: 2.1.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.1
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Tug: 1.0
ChimeraX-UI: 1.18.3
ChimeraX-uniprot: 2.2
ChimeraX-UnitCell: 1.0
ChimeraX-ViewDockX: 1.1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0
ChimeraX-WebServices: 1.1.0
ChimeraX-Zone: 1.0
colorama: 0.4.4
comtypes: 1.1.10
cxservices: 1.2
cycler: 0.11.0
Cython: 0.29.26
debugpy: 1.6.0
decorator: 5.1.1
docutils: 0.17.1
entrypoints: 0.4
filelock: 3.4.2
fonttools: 4.33.3
funcparserlib: 1.0.0
grako: 3.16.5
h5py: 3.7.0
html2text: 2020.1.16
idna: 3.3
ihm: 0.27
imagecodecs: 2021.11.20
imagesize: 1.3.0
ipykernel: 6.6.1
ipython: 7.31.1
ipython-genutils: 0.2.0
jedi: 0.18.1
Jinja2: 3.0.3
jupyter-client: 7.1.0
jupyter-core: 4.10.0
kiwisolver: 1.4.2
line-profiler: 3.4.0
lxml: 4.7.1
lz4: 3.1.10
MarkupSafe: 2.1.1
matplotlib: 3.5.1
matplotlib-inline: 0.1.3
msgpack: 1.0.3
nest-asyncio: 1.5.5
netCDF4: 1.5.8
networkx: 2.6.3
numexpr: 2.8.1
numpy: 1.22.1
openvr: 1.16.802
packaging: 21.3
ParmEd: 3.4.3
parso: 0.8.3
pickleshare: 0.7.5
Pillow: 9.0.1
pip: 21.3.1
pkginfo: 1.8.2
prompt-toolkit: 3.0.29
psutil: 5.9.0
pycollada: 0.7.2
pydicom: 2.2.2
Pygments: 2.11.2
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
PyQt6-commercial: 6.3.0
PyQt6-Qt6: 6.3.0
PyQt6-sip: 13.3.1
PyQt6-WebEngine-commercial: 6.3.0
PyQt6-WebEngine-Qt6: 6.3.0
python-dateutil: 2.8.2
pytz: 2022.1
pywin32: 303
pyzmq: 23.1.0
qtconsole: 5.3.0
QtPy: 2.1.0
RandomWords: 0.3.0
requests: 2.27.1
scipy: 1.7.3
setuptools: 59.8.0
sfftk-rw: 0.7.2
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
Sphinx: 4.3.2
sphinx-autodoc-typehints: 1.15.2
sphinxcontrib-applehelp: 1.0.2
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
suds-community: 1.0.0
tables: 3.7.0
tifffile: 2021.11.2
tinyarray: 1.2.4
tornado: 6.1
traitlets: 5.1.1
urllib3: 1.26.9
wcwidth: 0.2.5
webcolors: 1.11.1
wheel: 0.37.1
wheel-filename: 1.3.0
WMI: 1.5.1
Change History (2)
comment:1 by , 8 months ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Sessions |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → MemoryError saving map in session |
comment:2 by , 8 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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