MemoryError saving session

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\Anthony Bochler\\\Desktop\\\Thèse\\\Images\\\ribo-TC-
> yeast-coli.cxs"

opened ChimeraX session  

> open "C:/Users/Anthony Bochler/Desktop/Thèse/Images/PDB/43s+ddx-
> noATP+GMP-1704.pdb"

Summary of feedback from opening C:/Users/Anthony
Bochler/Desktop/Thèse/Images/PDB/43s+ddx-noATP+GMP-1704.pdb  
---  
warnings | Ignored bad PDB record found on line 635  
TER ***** ZN e 301  
  
Duplicate atom serial number found: 26426  
Ignored bad PDB record found on line 136188  
TER ***** U 02323  
  
Chain information for 43s+ddx-noATP+GMP-1704.pdb #5  
---  
Chain | Description  
0 | No description available  
1 | No description available  
5 | No description available  
8 | No description available  
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  
J | No description available  
K | No description available  
L | No description available  
M | No description available  
N | No description available  
O | No description available  
P | No description available  
Q | No description available  
R | No description available  
S | No description available  
T | No description available  
U | No description available  
V | No description available  
W | No description available  
X | No description available  
Y | No description available  
Z | No description available  
a | No description available  
b | No description available  
c | No description available  
d | No description available  
f | No description available  
g | No description available  
h | No description available  
i | No description available  
j | No description available  
l | No description available  
m | No description available  
n | No description available  
o | No description available  
p | No description available  
q | No description available  
r | No description available  
s | No description available  
t | No description available  
u | No description available  
v | No description available  
w | No description available  
y | No description available  
  

> hide #!2 models

> hide #5.1 models

> show #5.1 models

> select #5.1

10 pseudobonds, 1 model selected  

> select #5/W:56@CG2

1 atom, 1 model selected  

> ui mousemode rightMode pivot

> select #5/W:51@O

1 atom, 1 model selected  

> select #5/0:1326@C5'

1 atom, 1 model selected  

> select up

23 atoms, 25 bonds, 1 model selected  

> select up

45795 atoms, 51207 bonds, 1 model selected  

> color #5/0 white

> select #5/C:107@N

1 atom, 1 model selected  

> select up

66 atoms, 62 bonds, 1 model selected  

> select up

694 atoms, 704 bonds, 1 model selected  

> select up

22489 atoms, 22898 bonds, 1 model selected  

> color #5/0 #eb0026

> color #5/0 white

> color sel #eb0026

> select #5/A:8@CG2

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 1 model selected  

> select up

330 atoms, 341 bonds, 1 model selected  

> select up

3894 atoms, 3974 bonds, 1 model selected  

> color sel #ffa100

> select #5/Y:312@NH2

1 atom, 1 model selected  

> select up

11 atoms, 10 bonds, 1 model selected  

> select up

193 atoms, 192 bonds, 1 model selected  

> select #5/5:339@CG1

1 atom, 1 model selected  

> select up

7 atoms, 6 bonds, 1 model selected  

> select up

48 atoms, 49 bonds, 1 model selected  

> select up

3246 atoms, 3304 bonds, 1 model selected  

> color sel orange

> select #5/1:62@O2'

1 atom, 1 model selected  

> select up

22 atoms, 24 bonds, 1 model selected  

> select up

1606 atoms, 1798 bonds, 1 model selected  

> color sel #c70066

> select #5/V:70@CG2

1 atom, 1 model selected  

> select up

7 atoms, 6 bonds, 1 model selected  

> select up

110 atoms, 112 bonds, 1 model selected  

> select up

790 atoms, 800 bonds, 1 model selected  

> select #5/n:161@N

1 atom, 1 model selected  

> select up

9 atoms, 8 bonds, 1 model selected  

> select up

39 atoms, 38 bonds, 1 model selected  

> select up

1798 atoms, 1820 bonds, 1 model selected  

> color sel red

> select #5/V:51@CE2

1 atom, 1 model selected  

> select up

11 atoms, 11 bonds, 1 model selected  

> select up

70 atoms, 70 bonds, 1 model selected  

> select up

790 atoms, 800 bonds, 1 model selected  

> color sel #30ffc7

> select #5/C:106@O

1 atom, 1 model selected  

> select up

13404 atoms, 13560 bonds, 1 model selected  

> select up

16831 atoms, 17131 bonds, 1 model selected  

> select up

26383 atoms, 26872 bonds, 1 model selected  

> color sel #ff0d0d

> select #5/n:239@N

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 1 model selected  

> select up

45 atoms, 46 bonds, 1 model selected  

> select up

1798 atoms, 1820 bonds, 1 model selected  

> color sel #a62929

> select #5/0:48@N2

1 atom, 1 model selected  

> select up

23 atoms, 25 bonds, 1 model selected  

> select up

45795 atoms, 51207 bonds, 1 model selected  

> select #5/Y:253@CG1

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 1 model selected  

> select up

77 atoms, 76 bonds, 1 model selected  

> select up

1388 atoms, 1407 bonds, 1 model selected  

> color sel #00ab24

> select #5/w:150@CA

1 atom, 1 model selected  

> select up

9 atoms, 8 bonds, 1 model selected  

> select up

469 atoms, 475 bonds, 1 model selected  

> select up

1162 atoms, 1177 bonds, 1 model selected  

> color sel #3050f8

> select clear

> save session "C:/Users/Anthony Bochler/Desktop/Thèse/Images/ribo-TC-yeast-
> coli.cxs"

> select #5/a:50@CD

1 atom, 1 model selected  

> select up

115 atoms, 104 bonds, 1 model selected  

> select up

1950 atoms, 1969 bonds, 1 model selected  

> select up

14750 atoms, 15004 bonds, 1 model selected  

> select up

14769 atoms, 15021 bonds, 1 model selected  

> select up

14949 atoms, 15205 bonds, 1 model selected  

> select up

18149 atoms, 18472 bonds, 1 model selected  

> color sel #575961

> select #5/f:254@C

1 atom, 1 model selected  

> select up

9 atoms, 8 bonds, 1 model selected  

> select up

58 atoms, 60 bonds, 1 model selected  

> select up

12259 atoms, 12512 bonds, 1 model selected  

> hide #5/f

> select #5/y:101@CB

1 atom, 1 model selected  

> select up

25 atoms, 22 bonds, 1 model selected  

> select up

287 atoms, 288 bonds, 1 model selected  

> select up

2768 atoms, 2817 bonds, 1 model selected  

> select up

2777 atoms, 2825 bonds, 1 model selected  

> select up

3089 atoms, 3144 bonds, 1 model selected  

> select up

3884 atoms, 3954 bonds, 1 model selected  

> select up

3893 atoms, 3962 bonds, 1 model selected  

> select up

4089 atoms, 4160 bonds, 1 model selected  

> select up

4514 atoms, 4595 bonds, 1 model selected  

> select up

4525 atoms, 4605 bonds, 1 model selected  

> select up

4540 atoms, 4620 bonds, 1 model selected  

> select up

6296 atoms, 6405 bonds, 1 model selected  

> color sel #575961

> select #5/c:21@CG2

1 atom, 1 model selected  

> select up

7 atoms, 6 bonds, 1 model selected  

> select up

125 atoms, 126 bonds, 1 model selected  

> select up

480 atoms, 488 bonds, 1 model selected  

> select up

530 atoms, 534 bonds, 1 model selected  

> select up

813 atoms, 821 bonds, 1 model selected  

> select up

8036 atoms, 8175 bonds, 1 model selected  

> color sel #575961

> select #5/b:44@CE1

1 atom, 1 model selected  

> select up

10 atoms, 10 bonds, 1 model selected  

> select up

94 atoms, 95 bonds, 1 model selected  

> select up

1019 atoms, 1037 bonds, 1 model selected  

> select up

136895 atoms, 144093 bonds, 1 model selected  

> select down

1019 atoms, 1037 bonds, 1 model selected  

> color sel #575961

> select #5/Q:13@CA

1 atom, 1 model selected  

> select up

56 atoms, 51 bonds, 1 model selected  

> select up

678 atoms, 685 bonds, 1 model selected  

> color sel #575961

> select up

2587 atoms, 2626 bonds, 1 model selected  

> color sel #575961

> select clear

> save session "C:/Users/Anthony Bochler/Desktop/Thèse/Images/ribo-TC-yeast-
> coli.cxs"

> lighting full

> lighting soft

> select #5/U:102@CG

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 1 model selected  

> select up

100 atoms, 99 bonds, 1 model selected  

> select up

526 atoms, 527 bonds, 1 model selected  

> color sel #575961

> select clear

Expected a keyword  

> save image eIFs-colored.tiff format tiff transparentBackground true

[Errno 13] Permission denied: 'eIFs-colored.tiff'  

> style #!5 ball

Changed 136895 atom styles  

> style #!5 stick

Changed 136895 atom styles  

> style #!5 sphere

Changed 136895 atom styles  

> save image eIFs-colored.tiff transparentBackground true

[Errno 13] Permission denied: 'eIFs-colored.tiff'  

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/eIFs-colored-
> parasite.tif" width 1341 height 825

> set bgColor white

> set bgColor gray

> set bgColor white

> set bgColor transparent

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/eIFs-colored-
> parasite.tif" width 1341 height 825

> set bgColor white

> graphics silhouettes true

> lighting shadows true intensity 0.5

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting shadows false

> lighting full

> lighting shadows false

> lighting shadows true

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/eIFs-colored-
> parasite.tif" width 1341 height 825

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/eIFs-colored-
> parasite-90°.tif" width 1341 height 825

> select #5

136895 atoms, 144093 bonds, 10 pseudobonds, 2 models selected  

> show sel surfaces

> select #5/f:1296@CA

1 atom, 1 model selected  

> hide #5/f

Expected ',' or a keyword  

> select #5/f:1302@ND2

1 atom, 1 model selected  

> select up

8 atoms, 7 bonds, 2 models selected  

> select up

134 atoms, 136 bonds, 2 models selected  

> select up

12259 atoms, 12512 bonds, 2 models selected  

Expected ',' or a keyword  

Expected ',' or a keyword  

Expected ',' or a keyword  

> hide sel

> surface hide #5/f

> hide #!5 models

> show #!4 models

> select #4/C1:540@C3'

1 atom, 1 model selected  

> select up

23 atoms, 25 bonds, 1 model selected  

> select up

38107 atoms, 42619 bonds, 1 model selected  

> select up

38814 atoms, 42619 bonds, 1 model selected  

> color sel #ffd123

> show sel surfaces

> show sel surfaces

> view

> hide #4/C1

> select clear

> select #4/C1:528@C6

1 atom, 1 model selected  

> select up

20 atoms, 21 bonds, 2 models selected  

> select up

38107 atoms, 42619 bonds, 2 models selected  

> select up

38814 atoms, 42619 bonds, 2 models selected  

> color sel #ffd123

> select clear

> select #4/D1:3028@C5'

1 atom, 1 model selected  

> select up

23 atoms, 25 bonds, 2 models selected  

> hide #4/D1

> select up

68577 atoms, 76764 bonds, 2 models selected  

> select up

70152 atoms, 76764 bonds, 2 models selected  

> color sel #006bff

> color sel #2194D6

> select clear

> select #4/DC:340@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> select up

641 atoms, 639 bonds, 2 models selected  

> select up

1798 atoms, 1789 bonds, 2 models selected  

> select up

1888 atoms, 1867 bonds, 17 models selected  

> select up

6042 atoms, 6322 bonds, 17 models selected  

> select up

15177 atoms, 15372 bonds, 17 models selected  

> select up

15244 atoms, 15425 bonds, 26 models selected  

> select up

19117 atoms, 19690 bonds, 26 models selected  

> select up

23147 atoms, 23641 bonds, 26 models selected  

> color sel #d9ffff

> select up

23157 atoms, 23649 bonds, 28 models selected  

> select up

23256 atoms, 23748 bonds, 28 models selected  

> select up

24556 atoms, 25048 bonds, 28 models selected  

> select up

24582 atoms, 25063 bonds, 32 models selected  

> select up

25174 atoms, 25655 bonds, 32 models selected  

> select up

28843 atoms, 29315 bonds, 32 models selected  

> color sel #d9ffff

> select up

28853 atoms, 29323 bonds, 35 models selected  

> select up

28888 atoms, 29358 bonds, 35 models selected  

> select up

29188 atoms, 29658 bonds, 35 models selected  

> color sel #d9ffff

> select #4/B2,B3

6086 atoms, 6629 bonds, 305 pseudobonds, 3 models selected  

> select #4/B2

2649 atoms, 2883 bonds, 158 pseudobonds, 3 models selected  

> select #4/D2

2642 atoms, 2883 bonds, 150 pseudobonds, 3 models selected  

> color sel #2194D6

> select #4/D3

3437 atoms, 3746 bonds, 148 pseudobonds, 3 models selected  

> color sel #2194D6

> select #4/Cd:91@CB

1 atom, 1 model selected  

> select up

70 atoms, 56 bonds, 15 models selected  

> select up

1375 atoms, 1359 bonds, 15 models selected  

> select up

10214 atoms, 10181 bonds, 15 models selected  

> select up

10233 atoms, 10196 bonds, 19 models selected  

> select up

10730 atoms, 10693 bonds, 19 models selected  

> select up

11848 atoms, 11811 bonds, 19 models selected  

> color sel #ffff30

> color sel #ffd98f

> select #4/Dg:85@CA

1 atom, 1 model selected  

> select up

35 atoms, 28 bonds, 8 models selected  

> select up

717 atoms, 709 bonds, 8 models selected  

> select up

2961 atoms, 2932 bonds, 8 models selected  

> color sel #ffd98f

> select up

309610 atoms, 331239 bonds, 8 models selected  

> select down

2961 atoms, 2932 bonds, 67 models selected  

> select #4/CJ:24@CB

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> select up

142 atoms, 141 bonds, 2 models selected  

> select up

658 atoms, 657 bonds, 2 models selected  

> color sel #ffd98f

> select #4/CF:69@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> select up

24 atoms, 23 bonds, 2 models selected  

> select up

382 atoms, 381 bonds, 2 models selected  

> color sel #ffd98f

> select clear

> select #4/Di:12@CA

1 atom, 1 model selected  

> select up

5 atoms, 4 bonds, 2 models selected  

> select up

25 atoms, 24 bonds, 2 models selected  

> select up

60 atoms, 59 bonds, 2 models selected  

> color sel #ffff30

> color sel #d9ffff

> select clear

> select #4/C1:440@N3

1 atom, 1 model selected  

> select up

20 atoms, 21 bonds, 2 models selected  

> select up

38107 atoms, 42619 bonds, 2 models selected  

> select clear

> graphics silhouettes false

> graphics silhouettes true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting shadows false

> lighting shadows true

> lighting full

> lighting soft

> lighting full

> lighting simple

> lighting soft

> lighting full

> lighting soft

> show #!2 models

> hide #!2 models

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting soft

> lighting full

> lighting soft

> save image 80S-yeast.tiff format tiff transparentBackground true

[Errno 13] Permission denied: '80S-yeast.tiff'  

> save image 80S-yeast.tiff format tiff transparentBackground true

[Errno 13] Permission denied: '80S-yeast.tiff'  

> save image 80S-yeast.tif format tiff transparentBackground true

[Errno 13] Permission denied: '80S-yeast.tif'  

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast.tif"
> width 1341 height 825

Expected an axis vector or a keyword  

> turn x 180

> turn y 180

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-180.tif"
> width 1341 height 802

> toolshed show "Side View"

> lighting full

> lighting soft

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-EPA-
> sites.tif" width 1341 height 802

> save session "C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-EPA-
> sites.cxs"

> save session "C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-SSU-
> side.cxs"

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/80S-yeast-SSU-
> side.tif" width 1341 height 802

> hide #!4 models

> show #!3 models

Unknown command: load 5LI0  

> open 5LI0

Summary of feedback from opening 5LI0 fetched from pdb  
---  
notes | Fetching compressed mmCIF 5li0 from
http://files.rcsb.org/download/5li0.cif  
Fetching CCD MG from http://ligand-expo.rcsb.org/reports/M/MG/MG.cif  
Fetching CCD O from http://ligand-expo.rcsb.org/reports/O/O/O.cif  
Fetching CCD ZN from http://ligand-expo.rcsb.org/reports/Z/ZN/ZN.cif  
  
5li0 title:  
70S ribosome from Staphylococcus aureus [more info...]  
  
Chain information for 5li0 #6  
---  
Chain | Description  
0 | 50S ribosomal protein L28  
1 | 50S ribosomal protein L29  
2 | 50S ribosomal protein L30  
3 | 50S ribosomal protein L31 type B  
4 | 50S ribosomal protein L32  
5 | 50S ribosomal protein L33 2  
6 | 50S ribosomal protein L34  
7 | 50S ribosomal protein L35  
8 | 50S ribosomal protein L36  
A | 23S ribosomal RNA  
B | 5S ribosomal RNA  
D | 50S ribosomal protein L2  
E | 50S ribosomal protein L3  
F | 50S ribosomal protein L4  
G | 50S ribosomal protein L5  
H | 50S ribosomal protein L6  
M | 50S ribosomal protein L13  
N | 50S ribosomal protein L14  
O | 50S ribosomal protein L15  
P | 50S ribosomal protein L16  
Q | 50S ribosomal protein L17  
R | 50S ribosomal protein L18  
S | 50S ribosomal protein L19  
T | 50S ribosomal protein L20  
U | 50S ribosomal protein L21  
V | 50S ribosomal protein L22  
W | 50S ribosomal protein L23  
X | 50S ribosomal protein L24  
Y | 50S ribosomal protein L25  
Z | 50S ribosomal protein L27  
a | 16S ribosomal RNA  
b | 30S ribosomal protein S2  
c | 30S ribosomal protein S3  
d | 30S ribosomal protein S4  
e | 30S ribosomal protein S5  
f | 30S ribosomal protein S6  
g | 30S ribosomal protein S7  
h | 30S ribosomal protein S8  
i | 30S ribosomal protein S9  
j | 30S ribosomal protein S10  
k | 30S ribosomal protein S11  
l | 30S ribosomal protein S12  
m | 30S ribosomal protein S13  
n | 30S ribosomal protein S14 type Z  
o | 30S ribosomal protein S15  
p | 30S ribosomal protein S16  
q | 30S ribosomal protein S17  
r | 30S ribosomal protein S18  
s | 30S ribosomal protein S19  
t | 30S ribosomal protein S20  
  
Non-standard residues in 5li0 #6  
---  
MG — magnesium ion  
O — oxygen atom  
ZN — zinc ion  
  
  

> hide #!3 models

> select #6

140825 atoms, 152930 bonds, 4526 pseudobonds, 4 models selected  

> show sel surfaces

> hide #6/a

> select #6/a:425@O2'

1 atom, 1 model selected  

> select up

23 atoms, 25 bonds, 2 models selected  

> select up

33126 atoms, 37086 bonds, 2 models selected  

> select up

33140 atoms, 37086 bonds, 2 models selected  

> color sel #ffd123

> color sel #ffd98f

> color sel #ffd123

> select #6/s:21@CB

1 atom, 1 model selected  

> select up

72 atoms, 62 bonds, 11 models selected  

> select up

1133 atoms, 1133 bonds, 11 models selected  

> select up

11098 atoms, 11256 bonds, 11 models selected  

> select up

11179 atoms, 11329 bonds, 19 models selected  

> select up

11865 atoms, 12024 bonds, 19 models selected  

> select up

18051 atoms, 18307 bonds, 19 models selected  

> color sel #ffd98f

> select #6/n:22@CG2

1 atom, 1 model selected  

> select up

15 atoms, 13 bonds, 3 models selected  

> select up

389 atoms, 395 bonds, 3 models selected  

> select up

1179 atoms, 1206 bonds, 3 models selected  

> color sel #ffd98f

> select #6/A:1142@C1'

1 atom, 1 model selected  

> select up

22 atoms, 24 bonds, 2 models selected  

> select up

62475 atoms, 69965 bonds, 2 models selected  

> color sel #2194D6

> select #6/B:62@O2'

1 atom, 1 model selected  

> select up

20 atoms, 21 bonds, 2 models selected  

> select up

2427 atoms, 2714 bonds, 2 models selected  

> color sel #2194D6

> select #6/S:42@CG2

1 atom, 1 model selected  

> select up

153 atoms, 135 bonds, 20 models selected  

> select up

2254 atoms, 2263 bonds, 20 models selected  

> select up

18239 atoms, 18463 bonds, 20 models selected  

> select up

18248 atoms, 18471 bonds, 21 models selected  

> select up

18288 atoms, 18511 bonds, 21 models selected  

> select up

18468 atoms, 18693 bonds, 21 models selected  

> select up

18500 atoms, 18721 bonds, 24 models selected  

> select up

18679 atoms, 18902 bonds, 24 models selected  

> select up

20105 atoms, 20344 bonds, 24 models selected  

> color sel #b3e3f5

> select clear

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/70S-staph.tif"
> width 1341 height 802

> turn y 180

> lighting full

> lighting soft

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/70S-staph-180.tif"
> width 1341 height 802

> save session "C:/Users/Anthony Bochler/Desktop/Thèse/Images/70S-staph.cxs"

> hide #!6 models

> show #!2 models

> select #2

239041 atoms, 257813 bonds, 5 pseudobonds, 2 models selected  

> show sel surfaces

> select #2/E:521@C5'

1 atom, 1 model selected  

> select up

22 atoms, 24 bonds, 2 models selected  

> select up

53434 atoms, 59734 bonds, 2 models selected  

> select up

239041 atoms, 257813 bonds, 2 models selected  

> select down

53434 atoms, 59734 bonds, 50 models selected  

> select #2/E:704@O2P

1 atom, 1 model selected  

> select up

22 atoms, 24 bonds, 2 models selected  

> select up

53434 atoms, 59734 bonds, 2 models selected  

> color sel #ffd98f

> color sel #ffd123

> select #2/M:140@O

1 atom, 1 model selected  

> select up

118 atoms, 109 bonds, 14 models selected  

> select up

3880 atoms, 3954 bonds, 14 models selected  

> select up

31993 atoms, 32600 bonds, 14 models selected  

> color sel #ffd98f

> select #2/Y:103@CE

1 atom, 1 model selected  

> select up

61 atoms, 53 bonds, 9 models selected  

> select up

4612 atoms, 4689 bonds, 9 models selected  

> select up

4692 atoms, 4762 bonds, 16 models selected  

> select up

9579 atoms, 9730 bonds, 16 models selected  

> select up

35224 atoms, 35819 bonds, 16 models selected  

> color sel #ffd98f

> select #2/O:19@OG1

1 atom, 1 model selected  

> select up

18 atoms, 16 bonds, 3 models selected  

> select up

923 atoms, 939 bonds, 3 models selected  

> select up

5072 atoms, 5156 bonds, 3 models selected  

> select up

239041 atoms, 257813 bonds, 3 models selected  

> color sel #ffd98f

> hide #!2 models

> show #!4 models

> hide #!4 models

> show #!2 models

> select up

108670 atoms, 117066 bonds, 2 pseudobonds, 47 models selected  

> select up

193780 atoms, 211756 bonds, 2 pseudobonds, 47 models selected  

> select down

108670 atoms, 117066 bonds, 2 pseudobonds, 47 models selected  

> select clear

> color sel #b3e3f5

> color sel #b3e3f5

> color sel #b3e3f5

> color sel #b3e3f5

> color sel #b3e3f5

> color sel #b3e3f5

> select #2/B:329@P

1 atom, 1 model selected  

> select #2/E

53434 atoms, 59734 bonds, 1 pseudobond, 2 models selected  

> color sel #ffd123

> color sel #b3e3f5

> select #2/A:1909@O2

1 atom, 1 model selected  

> select up

20 atoms, 21 bonds, 2 models selected  

> select up

42172 atoms, 47209 bonds, 2 models selected  

> color sel #2196D6

> select #2/B:232@P

1 atom, 1 model selected  

> select up

20 atoms, 21 bonds, 2 models selected  

> select up

34483 atoms, 38561 bonds, 2 models selected  

> color sel #2196D6

> color sel #b3e3f5

> color sel #b3e3f5

> select #2/G:40@O2'

1 atom, 1 model selected  

> select up

20 atoms, 21 bonds, 2 models selected  

> select up

1543 atoms, 1722 bonds, 2 models selected  

> color sel #2196D6

> select up

239041 atoms, 257813 bonds, 2 models selected  

> select down

1543 atoms, 1722 bonds, 50 models selected  

> select clear

> select #2/H:62@O2'

1 atom, 1 model selected  

> select up

23 atoms, 25 bonds, 2 models selected  

> select up

2836 atoms, 3169 bonds, 2 models selected  

> select up

239041 atoms, 257813 bonds, 2 models selected  

> select up

239041 atoms, 257813 bonds, 5 pseudobonds, 51 models selected  

> select down

239041 atoms, 257813 bonds, 50 models selected  

> select down

2836 atoms, 3169 bonds, 50 models selected  

> color sel #2196D6

> select #2/F:129@O2'

1 atom, 1 model selected  

> select up

23 atoms, 25 bonds, 2 models selected  

> select up

3806 atoms, 4256 bonds, 2 models selected  

> color sel #2196D6

> select clear

> save image "C:/Users/Anthony Bochler/Desktop/Thèse/Images/90S-kineto.tif"
> width 1341 height 802

> color sel #ffd123

> color sel #ffd98f

> select clear

> save image "C:/Users/Anthony
> Bochler/Desktop/Thèse/Images/90S-kineto-180.tif" width 1341 height 802

> save session "C:/Users/Anthony Bochler/Desktop/Thèse/Images/ribo-kineto-
> blueyellow.cxs"

Traceback (most recent call last):  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 796,
in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 561,
in save  
fserialize(stream, data)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\serialize.py", line 63,
in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 284, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 290, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 287, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\_packer.pyx", line 277, in msgpack._cmsgpack.Packer._pack  
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap  
File "_serialize.pyx", line 242, in core._serialize._encode_ext  
File "msgpack\\_packer.pyx", line 284, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 290, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 287, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\_packer.pyx", line 263, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\_packer.pyx", line 277, in msgpack._cmsgpack.Packer._pack  
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap  
File "_serialize.pyx", line 215, in core._serialize._encode_ext  
File "msgpack\\_packer.pyx", line 284, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 290, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 287, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 911, in
<lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 641, in
file_save_cb  
self.save_dialog.display(self, session)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\ui\save_dialog.py", line 139,
in display  
fmt.save(session, filename)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 1100,
in save  
run(session, cmd)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
31, in run  
results = command.run(text, log=log)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2837, in run  
result = ci.function(session, **kw_args)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 992,
in save_session  
save(session, filename, **kw)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\save.py", line
61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 229, in
export  
result = self.export_func(session, path, **kw)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 796,
in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 561,
in save  
fserialize(stream, data)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\serialize.py", line 63,
in msgpack_serialize  
stream.write(packer.pack(obj))  
File "msgpack\\_packer.pyx", line 284, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 290, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 287, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\_packer.pyx", line 277, in msgpack._cmsgpack.Packer._pack  
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap  
File "_serialize.pyx", line 242, in core._serialize._encode_ext  
File "msgpack\\_packer.pyx", line 284, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 290, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 287, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\_packer.pyx", line 263, in msgpack._cmsgpack.Packer._pack  
File "msgpack\\_packer.pyx", line 277, in msgpack._cmsgpack.Packer._pack  
File "stringsource", line 67, in
cfunc.to_py.__Pyx_CFunc_object____object___to_py.wrap  
File "_serialize.pyx", line 215, in core._serialize._encode_ext  
File "msgpack\\_packer.pyx", line 284, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 290, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 287, in msgpack._cmsgpack.Packer.pack  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
MemoryError  
  
MemoryError  
  
File "msgpack\\_packer.pyx", line 234, in msgpack._cmsgpack.Packer._pack  
  
See log for complete Python traceback.  
  

> save session "C:/Users/Anthony Bochler/Desktop/Thèse/Images/ribo-kineto-
> blueyellow.cxs"

Traceback (most recent call last):  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 796,
in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 556,
in save  
mgr.discovery(self._state_containers)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 255,
in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 288,
in process  
return copy_state(data, convert=convert)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 210, in
copy_state  
return _copy(data)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 195, in
_copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 195, in
<listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 198, in
_copy  
return data.copy()  
MemoryError: Unable to allocate array with shape (191951, 3) and data type
float32  
  
MemoryError: Unable to allocate array with shape (191951, 3) and data type
float32  
  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 198, in
_copy  
return data.copy()  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 911, in
<lambda>  
save_action.triggered.connect(lambda arg, s=self, sess=session:
s.file_save_cb(sess))  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py", line 641, in
file_save_cb  
self.save_dialog.display(self, session)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\ui\save_dialog.py", line 139,
in display  
fmt.save(session, filename)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 1100,
in save  
run(session, cmd)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\run.py", line
31, in run  
results = command.run(text, log=log)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py", line
2837, in run  
result = ci.function(session, **kw_args)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 992,
in save_session  
save(session, filename, **kw)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\commands\save.py", line
61, in save  
fmt.export(session, filename, fmt.nicknames[0], **kw)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\io.py", line 229, in
export  
result = self.export_func(session, path, **kw)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 796,
in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 556,
in save  
mgr.discovery(self._state_containers)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 255,
in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\session.py", line 288,
in process  
return copy_state(data, convert=convert)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 210, in
copy_state  
return _copy(data)  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 195, in
_copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 195, in
<listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 198, in
_copy  
return data.copy()  
MemoryError: Unable to allocate array with shape (191951, 3) and data type
float32  
  
MemoryError: Unable to allocate array with shape (191951, 3) and data type
float32  
  
File "C:\ChimeraX\bin\lib\site-packages\chimerax\core\state.py", line 198, in
_copy  
return data.copy()  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 432.00
OpenGL renderer: GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[pett]

Doubtful anything can be done.

[Greg Couch]

Not sure if this is the same bug, but the msgpack size limits have been set to the maximum possible values. And future bug reports will list the size of the RAM.