MemoryError saving map in session

[chimerax-bug-report@…]

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