Opened 3 years ago

Closed 3 years ago

#8703 closed defect (limitation)

MemoryError saving session

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22621
ChimeraX Version: 1.5rc202211120143 (2022-11-12 01:43:47 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5rc202211120143 (2022-11-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Extended_fugure\\\beta-
> ADP.cxs

Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at
level 0.0721, step 1, values float32  
Log from Mon Mar 13 22:44:38 2023UCSF ChimeraX version: 1.5rc202211120143
(2022-11-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Extended_fugure\\\beta-
> ADP.cxs

Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at
level 0.0721, step 1, values float32  
Log from Tue Feb 7 16:56:44 2023UCSF ChimeraX version: 1.5rc202211120143
(2022-11-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Figure2\\\beta_D1-D5.cxs

Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at
level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 0 as #3.1, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 1 as #3.2, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 2 as #3.3, grid size 450,450,450, pixel 1.07, shown
at level 0.006, step 1, values float32  
Opened 1254_global_2.9.mrc 3 as #3.4, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 4 as #3.5, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 5 as #3.6, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 6 as #3.7, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 7 as #3.8, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 8 as #3.9, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 9 as #3.10, grid size 450,450,450, pixel 1.07,
shown at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 10 as #3.11, grid size 450,450,450, pixel 1.07,
shown at level 0.0721, step 1, values float32  
Log from Fri Feb 3 18:52:14 2023UCSF ChimeraX version: 1.5rc202211120143
(2022-11-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Figure2\\\beta_D1-D5.cxs

Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at
level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 0 as #3.1, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 1 as #3.2, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 2 as #3.3, grid size 450,450,450, pixel 1.07, shown
at level 0.006, step 1, values float32  
Opened 1254_global_2.9.mrc 3 as #3.4, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 4 as #3.5, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 5 as #3.6, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 6 as #3.7, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 7 as #3.8, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 8 as #3.9, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 9 as #3.10, grid size 450,450,450, pixel 1.07,
shown at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 10 as #3.11, grid size 450,450,450, pixel 1.07,
shown at level 0.0721, step 1, values float32  
Log from Wed Feb 1 10:44:09 2023UCSF ChimeraX version: 1.5rc202211120143
(2022-11-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  

> open
> C:\\\Users\\\yangx\\\Desktop\\\PhK_figures\\\Figure2\\\beta_far_split.cxs

Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at
level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 0 as #3.1, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 1 as #3.2, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 2 as #3.3, grid size 450,450,450, pixel 1.07, shown
at level 0.006, step 1, values float32  
Opened 1254_global_2.9.mrc 3 as #3.4, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 4 as #3.5, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 5 as #3.6, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 6 as #3.7, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 7 as #3.8, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 8 as #3.9, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 9 as #3.10, grid size 450,450,450, pixel 1.07,
shown at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 10 as #3.11, grid size 450,450,450, pixel 1.07,
shown at level 0.0721, step 1, values float32  
Log from Tue Jan 31 14:40:14 2023UCSF ChimeraX version: 1.5rc202211120143
(2022-11-12)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> C:\\\ShareCache\\\肖俊宇_1406180305\\\Lab\\\杨晓珂_1801110533\\\5.20220614_hPhK_active_CALM\\\1254_active_Holo_tetramer_23_AGC-
> coot-14.pdb

Summary of feedback from opening
C:\\\ShareCache\\\肖俊宇_1406180305\\\Lab\\\杨晓珂_1801110533\\\5.20220614_hPhK_active_CALM\\\1254_active_Holo_tetramer_23_AGC-
coot-14.pdb  
---  
warnings | Start residue of secondary structure not found: HELIX 212 212 VAL A
767 LEU A 770 1 4  
Start residue of secondary structure not found: HELIX 233 233 GLY D 8 THR D 21
1 14  
Start residue of secondary structure not found: HELIX 234 234 LEU D 23 HIS D
25 1 3  
Start residue of secondary structure not found: HELIX 235 235 VAL D 44 SER D
50 1 7  
Start residue of secondary structure not found: HELIX 236 236 LEU D 52 ASN D
64 1 13  
118 messages similar to the above omitted  
  
Chain information for 1254_active_Holo_tetramer_23_AGC-coot-14.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C G K O | No description available  
E I M | No description available  
F J N | No description available  
  

> show cartoons

> show atoms

> hide atoms

> dssp

> select /A:6-1221

7587 atoms, 7745 bonds, 3 pseudobonds, 959 residues, 2 models selected  

> select /A /F /H /J

24364 atoms, 24904 bonds, 7 pseudobonds, 3030 residues, 2 models selected  

> select clear

> select /B:43-1093

8264 atoms, 8450 bonds, 2 pseudobonds, 1023 residues, 2 models selected  

> select /B:43-1093

8264 atoms, 8450 bonds, 2 pseudobonds, 1023 residues, 2 models selected  

> select /G:327-380

411 atoms, 420 bonds, 1 pseudobond, 49 residues, 2 models selected  

> select /G:327-380

411 atoms, 420 bonds, 1 pseudobond, 49 residues, 2 models selected  

> select /K:327-380

411 atoms, 420 bonds, 1 pseudobond, 49 residues, 2 models selected  

> select /O:327-380

411 atoms, 420 bonds, 1 pseudobond, 49 residues, 2 models selected  

> select /E:3-1221

7674 atoms, 7827 bonds, 6 pseudobonds, 970 residues, 2 models selected  

> select /I:3-1221

7674 atoms, 7827 bonds, 6 pseudobonds, 970 residues, 2 models selected  

> select /M:3-1221

7674 atoms, 7827 bonds, 6 pseudobonds, 970 residues, 2 models selected  

> select /F:6-1093

8366 atoms, 8556 bonds, 2 pseudobonds, 1034 residues, 2 models selected  

> select /J:6-1093

8366 atoms, 8556 bonds, 2 pseudobonds, 1034 residues, 2 models selected  

> select /N:6-1093

8366 atoms, 8556 bonds, 2 pseudobonds, 1034 residues, 2 models selected  

> select /b /F /N /J

33449 atoms, 34207 bonds, 8 pseudobonds, 4130 residues, 2 models selected  

> select /a /c /g /k /o /e /i /m

32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 2 models selected  

> hide sel cartoons

> set bgColor white

> lighting soft

> select /b

8306 atoms, 8494 bonds, 2 pseudobonds, 1025 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel dark green

> select /e

7689 atoms, 7844 bonds, 6 pseudobonds, 971 residues, 2 models selected  

> select /n

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> color sel dark sea green

> select /f

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> color sel lime green

> select /j

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> color sel medium sea green

> select clear

> select /j

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> color sel lime green

> select /n

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> select /f

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> color sel medium sea green

> select clear

> select 1101

Expected an objects specifier or a keyword  

> show atoms

> undo

> select /b:1101

15 atoms, 14 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /b:1090,1101

21 atoms, 20 bonds, 2 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 21 atom styles  

> color sel byhetero

> select /b:1090,1101 /f:1090,1101 /n:1090,1101 /j:1090,1101

84 atoms, 80 bonds, 8 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 84 atom styles  

> color sel byhetero

> select clear

> select /a /c /g /k /o /e /i /m

32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 2 models selected  

> show sel cartoons

> select /a /e /i /m

30669 atoms, 31294 bonds, 21 pseudobonds, 3873 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel goldenrod

> select /c /g /k /o

1644 atoms, 1680 bonds, 4 pseudobonds, 196 residues, 2 models selected  

> color sel medium turquoise

> select /a:1220,1301 /e:1220,1301 /i:1220,1301 /m:1220,1301

84 atoms, 88 bonds, 8 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 84 atom styles  

> color sel byhetero

> select clear

> select /a /c /g /k /o /e /i /m

32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 2 models selected  

> hide sel cartoons

> show sel cartoons

> select clear

> show surfaces

> hide surfaces

> select /a /c /g /k /o /e /i /m

32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> select up

65762 atoms, 67181 bonds, 33 pseudobonds, 8199 residues, 10 models selected  

> select down

32313 atoms, 32974 bonds, 25 pseudobonds, 4069 residues, 14 models selected  

> select /b:1090,1101 /f:1090,1101 /n:1090,1101 /j:1090,1101

84 atoms, 80 bonds, 8 residues, 1 model selected  

> show sel surfaces

> hide sel surfaces

> open C:/Users/yangx/Desktop/5.20220614_hPhK_active_CALM/1254_global_2.9.mrc

Opened 1254_global_2.9.mrc as #2, grid size 450,450,450, pixel 1.07, shown at
level 0.000934, step 2, values float32  

> volume #2 step 1

> volume #2 level 0.05581

> color (#!1 & sel) light gray

> ui tool show "Color Zone"

> color zone #2 near #1 distance 6.42

> volume #2 level 0.09913

> volume #2 level 0.2074

> volume #2 level 0.06935

> volume #2 level 0.07205

> color zone #2 near #1 distance 5

> volume splitbyzone #2

Opened 1254_global_2.9.mrc 0 as #3.1, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 1 as #3.2, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 2 as #3.3, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 3 as #3.4, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 4 as #3.5, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 5 as #3.6, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 6 as #3.7, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 7 as #3.8, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 8 as #3.9, grid size 450,450,450, pixel 1.07, shown
at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 9 as #3.10, grid size 450,450,450, pixel 1.07,
shown at level 0.0721, step 1, values float32  
Opened 1254_global_2.9.mrc 10 as #3.11, grid size 450,450,450, pixel 1.07,
shown at level 0.0721, step 1, values float32  

> hide #!3 models

> show #!3 models

> hide #!3.2 models

> hide #!3.4 models

> hide #!3.5 models

> hide #!3.8 models

> hide #!3.9 models

> hide #!3.10 models

> hide #!3.11 models

> hide #!3.7 models

> hide #!3.6 models

> hide #!3 models

> hide #!3.1 models

> show #!3.1 models

> hide #!3 models

> show #!3 models

> hide #!3.1 models

> hide #!3 models

> show #!3 models

> volume #3.3 level 0.01407

> select clear

> volume #3.3 level 0.009991

> volume #3.3 level 0.008

> volume #3.3 level 0.005

> volume #3.3 level 0.002

> ui tool show "Hide Dust"

> surface dust #3.3 size 6.42

> surface dust #3.3 size 4.73

> surface dust #3.3 size 3.06

> surface dust #3.3 size 2.76

> surface dust #3.3 size 2.78

> surface dust #3.3 size 2.8

> surface dust #3.3 size 2.82

> surface dust #3.3 size 2.43

> surface dust #3.3 size 2.73

[Repeated 1 time(s)]

> volume #3.3 level 0.006

> save C:/Users/yangx/Desktop/PhK_figures/Figure2/beta_far_split.cxs
> includeMaps true

——— End of log from Tue Jan 31 14:40:14 2023 ———

opened ChimeraX session  

> ui mousemode right "pick blobs"

> select /N:1045

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select /N:1046

9 atoms, 8 bonds, 1 residue, 1 model selected  

> ui mousemode right "pick blobs"

[Repeated 1 time(s)]

> ui mousemode right "translate selected atoms"

> ui mousemode right pivot

[Repeated 1 time(s)]

> ui mousemode right "translate selected atoms"

> ui mousemode right pivot

> ui mousemode right "pick blobs"

[Repeated 1 time(s)]

> undo

[Repeated 2 time(s)]

> select clear

> interfaces ~solvent

16 buried areas: N B 1845, M O 1775, E G 1775, I K 1775, F J 1768, A C 1720, B
A 1642, J I 1502, N M 1492, F E 1481, F A 1117, N I 961, J M 941, B E 921, J N
828, F B 822  

> ui dockable true "Chain Contacts"

> hide sel cartoons

> hide #!3 models

> hide sel atoms

> hide sel cartoons

> hide sel atoms

> show sel surfaces

> ui tool show "Color Actions"

> color sel dark green

> select clear

> lighting soft

> lighting full

> lighting simple

> lighting soft

> ui windowfill toggle

> undo

> show sel cartoons

> save C:/Users/yangx/Desktop/PhK_figures/Figure2/beta4.cxs

> hide sel cartoons

> hide sel atoms

> hide sel surfaces

> select /f:1090

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel cartoons

> select clear

> select /f:1090

6 atoms, 5 bonds, 1 residue, 1 model selected  

> show sel cartoons

> show sel atoms

> select clear

[Repeated 2 time(s)]

> select /F:1090

6 atoms, 5 bonds, 1 residue, 1 model selected  

> hide sel atoms

> ui tool show "Color Actions"

> color sel medium sea green

> select clear

> select /f:43-480

3546 atoms, 3636 bonds, 438 residues, 1 model selected  

> color sel teal

> select /f:481-690

1694 atoms, 1728 bonds, 210 residues, 1 model selected  

> color sel steel blue

> select /f:709-778

553 atoms, 561 bonds, 70 residues, 1 model selected  

> select /f:481-690

1694 atoms, 1728 bonds, 210 residues, 1 model selected  

> color sel steel blue

> select /f:709-778

553 atoms, 561 bonds, 70 residues, 1 model selected  

> color sel cadet blue

> select /f:779-917

1117 atoms, 1145 bonds, 139 residues, 1 model selected  

> color sel light slate gray

> select /f:924-1080

1283 atoms, 1306 bonds, 157 residues, 1 model selected  

> color sel slate gray

> select clear

> select /f:924-1080

1283 atoms, 1306 bonds, 157 residues, 1 model selected  

> color sel slate gray

> color sel light slate gray

> color sel slate gray

> color sel medium aquamarine

> color sel cornflower blue

> color sel dark cyan

> color sel medium aquamarine

> color sel royal blue

> color sel indigo

> color sel slate gray

> color sel medium blue

> color sel dark blue

> color sel cadet blue

> color sel medium aquamarine

> select clear

> save C:/Users/yangx/Desktop/PhK_figures/Figure2/beta_D1-D5.cxs

——— End of log from Wed Feb 1 10:44:09 2023 ———

opened ChimeraX session  

> select /b:43-480 /f:43-480 /n:43-480 /j:43-480

14184 atoms, 14544 bonds, 1752 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel teal

> select /b:481-690 /f:481-690 /n:481-690 /j:481-690

6714 atoms, 6848 bonds, 1 pseudobond, 832 residues, 2 models selected  

> select /b:709-778 /f:709-778 /n:709-778 /j:709-778

2199 atoms, 2231 bonds, 278 residues, 1 model selected  

> color sel cadet blue

> select /a:748-822 /e:748-822 /m:748-822 /i:748-822

1689 atoms, 1712 bonds, 7 pseudobonds, 207 residues, 2 models selected  

> select /b:779-917 /f:779-917 /n:779-917 /j:779-917

4468 atoms, 4580 bonds, 556 residues, 1 model selected  

> color sel sea green

> select /b:924-1080 /f:924-1080 /n:924-1080 /j:924-1080

5132 atoms, 5224 bonds, 628 residues, 1 model selected  

> color sel cornflower blue

> select /b:918-923,1081-1093 /f:918-923,1081-1093 /n:918-923,1081-1093
> /j:918-923,1081-1093

584 atoms, 584 bonds, 76 residues, 1 model selected  

> color sel cornflower blue

> select /b:1090,1101 /f:1090,1101 /n:1090,1101 /j:1090,1101

84 atoms, 80 bonds, 8 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select /f:1090,1101

21 atoms, 20 bonds, 2 residues, 1 model selected  

> show sel atoms

> color sel cornflower blue

> color (#!1 & sel) byhetero

> select clear

> select /f

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> view sel

> select clear

> save C:/Users/yangx/Desktop/PhK_figures/Figure2/beta_D1-D5.cxs

——— End of log from Fri Feb 3 18:52:14 2023 ———

opened ChimeraX session  

> show #!3 models

> hide #!3 models

> ui tool show "Color Zone"

> color zone #2 near #1 distance 1.07

> close #3

> show #!2 models

> color zone #2 near #1 distance 1.07

[Repeated 1 time(s)]

> color zone #2 near #1 distance 6

> select /b:6

27 atoms, 29 bonds, 1 residue, 1 model selected  

> show sel atoms

> select /f：6

Expected an objects specifier or a keyword  

> show sel atoms

> hide #!2 models

> select /f:6

27 atoms, 29 bonds, 1 residue, 1 model selected  

> show sel atoms

> style sel stick

Changed 27 atom styles  

> select /b:6

27 atoms, 29 bonds, 1 residue, 1 model selected  

> hide sel atoms

> select /f:6

27 atoms, 29 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) gray

> show #!2 models

> color zone #2 near #1 distance 6

> transparency (#!1 & sel) 70

> select clear

> transparency 70

> hide cartoons

> select /b: 556,578,579,795,798,799,859,211,213,214,274

105 atoms, 103 bonds, 11 residues, 1 model selected  

> show sel atoms

> hide sel atoms

> select /f: 556,578,579,795,798,799,859,211,213,214,274

105 atoms, 103 bonds, 11 residues, 1 model selected  

> show sel atoms

> style sel stick

Changed 105 atom styles  

> color (#!1 & sel) byhetero

> lighting full

> lighting shadows false

> select /f:6

27 atoms, 29 bonds, 1 residue, 1 model selected  

> color (#!1 & sel) byhetero

> select clear

> show cartoons

> transparency 30 cartoons

> select #2

4 models selected  

> select #2

4 models selected  

> select up

65762 atoms, 67181 bonds, 8199 residues, 5 models selected  

> select up

65762 atoms, 67181 bonds, 33 pseudobonds, 8199 residues, 18 models selected  

> select #2

4 models selected  

> select /f:43-100

453 atoms, 464 bonds, 58 residues, 1 model selected  

> hide sel cartoons

> select #2

4 models selected  

> select #2

4 models selected  

> select clear

> save C:/Users/yangx/Desktop/PhK_figures/Extended_fugure/beta-ADP.tif width
> 1857 height 1168 supersample 3

> save C:/Users/yangx/Desktop/PhK_figures/Extended_fugure/beta-ADP.cxs

——— End of log from Tue Feb 7 16:56:44 2023 ———

opened ChimeraX session  

> ui tool show "Hide Dust"

> surface dust #2 size 6.42

> surface dust #2 size 4.05

> save C:/Users/yangx/Desktop/PhK_figures/Extended_fugure/beta-ADP.tif width
> 1965 height 1152 supersample 3

> save C:/Users/yangx/Desktop/PhK_figures/Extended_fugure/beta-ADP.cxs

——— End of log from Mon Mar 13 22:44:38 2023 ———

opened ChimeraX session  

> close #2

> open C:/Users/yangx/Desktop/1254_global_2.9_bin_.mrc

Opened 1254_global_2.9_bin_.mrc as #2, grid size 900,900,900, pixel 0.535,
shown at step 1, values float32  

> volume #2 region 0,0,0,899,899,899 step 4

[Repeated 1 time(s)]

> volume #2 change image level -0.0004992,0 level 0.004475,0.8 level 1.271,1

> volume #2 level 0.06899

> volume #2 step 1

> ui tool show "Hide Dust"

> surface dust #2 size 13.57

> surface dust #2 size 5.62

> volume #2 level 0.05

> volume #2 level 0.06

> volume #2 level 0.07

> ui tool show "Color Zone"

> color zone #2 near #1 distance 5

> color single #2

> hide atoms

> color zone #2 near #1 distance 5

> color single #2

> undo

[Repeated 2 time(s)]

> color single #2

> hide #!1 models

> show #!1 models

> hide #!2 models

> select clear

> select up

2 atoms, 1 bond, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 2 models selected  

> color (#!1 & sel) light gray

> color (#!1 & sel) gray

> select clear

> select /f:1-480

3573 atoms, 3665 bonds, 1 pseudobond, 439 residues, 2 models selected  

> ui tool show "Color Actions"

> color sel teal

> select /f:481-690

1694 atoms, 1728 bonds, 210 residues, 1 model selected  

> color sel steel blue

> select /f:709-778

553 atoms, 561 bonds, 70 residues, 1 model selected  

> color sel cadet blue

> select /f:779-917

1117 atoms, 1145 bonds, 139 residues, 1 model selected  

> color sel cadet blue

> select /f:709-778

553 atoms, 561 bonds, 70 residues, 1 model selected  

> color sel medium sea green

> select /F:6@C2'

1 atom, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 2 models selected  

> color sel gray

> show #!2 models

> color zone #2 near #1 distance 5

> select clear

> transparency #1#2.2#!2 40

> transparency #1#2.2#!2 60

> transparency #1#2.2#!2 50

> transparency 0 cartoons

> transparency 10 cartoons

> select clear

> color #1#2.2#!2 byhetero

> select clear

> volume #2 level 0.08

> undo

> color zone #2 near #1 distance 5

> color single #2

> volume #2 level 0.09

> surface dust #2 size 9

> surface dust #2 size 1

> surface dust #2 size 10

> surface dust #2 size 1

> surface dust #2 size 15

> surface dust #2 size 1

> surface dust #2 size 10

> hide #!2 models

> select /f:709-778

553 atoms, 561 bonds, 70 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium sea green

> select /f:779-917

1117 atoms, 1145 bonds, 139 residues, 1 model selected  

> color sel cadet blue

> select /f:481-690

1694 atoms, 1728 bonds, 210 residues, 1 model selected  

> color sel steel blue

> select /f:30-480

3546 atoms, 3636 bonds, 438 residues, 1 model selected  

> color sel teal

> select /F:6@C2'

1 atom, 1 residue, 1 model selected  

> select up

27 atoms, 29 bonds, 1 residue, 2 models selected  

> color sel gray

> show #!2 models

> color zone #2 near #1 distance 5

> select clear

> color #1#2.2#!2 byhetero

> transparency #1#2.2#!2 50

> select /f

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> select ~sel

57381 atoms, 58610 bonds, 31 pseudobonds, 7164 residues, 6 models selected  

> color (#!1 & sel) light gray

> color zone #2 near #1 distance 5

> undo

[Repeated 4 time(s)]

> select /f

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> select ~sel

57381 atoms, 58610 bonds, 31 pseudobonds, 7164 residues, 6 models selected  

> color (#!1 & sel) light gray

> color zone #2 near #1 distance 5

> select /f:918-1101

1444 atoms, 1469 bonds, 177 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel sea green

> color zone #2 near #1 distance 5

> volume splitbyzone #2

Opened 1254_global_2.9_bin_.mrc 0 as #3.1, grid size 900,900,900, pixel 0.535,
shown at level 0.09, step 1, values float32  
Opened 1254_global_2.9_bin_.mrc 1 as #3.2, grid size 900,900,900, pixel 0.535,
shown at level 0.09, step 1, values float32  
Opened 1254_global_2.9_bin_.mrc 2 as #3.3, grid size 900,900,900, pixel 0.535,
shown at level 0.09, step 1, values float32  
Opened 1254_global_2.9_bin_.mrc 3 as #3.4, grid size 900,900,900, pixel 0.535,
shown at level 0.09, step 1, values float32  
Opened 1254_global_2.9_bin_.mrc 4 as #3.5, grid size 900,900,900, pixel 0.535,
shown at level 0.09, step 1, values float32  
Opened 1254_global_2.9_bin_.mrc 5 as #3.6, grid size 900,900,900, pixel 0.535,
shown at level 0.09, step 1, values float32  
Opened 1254_global_2.9_bin_.mrc 6 as #3.7, grid size 900,900,900, pixel 0.535,
shown at level 0.09, step 1, values float32  
Opened 1254_global_2.9_bin_.mrc 7 as #3.8, grid size 900,900,900, pixel 0.535,
shown at level 0.09, step 1, values float32  

> hide #!3.1 models

> hide #!3.2 models

> hide #!3.3 models

> show #!3.3 models

> hide #!3.4 models

> show #!3.4 models

> hide #!3.5 models

> show #!3.5 models

> hide #!3.7 models

> show #!3.7 models

> hide #!3.5 models

> show #!3.5 models

> hide #!3.6 models

> hide #!3.8 models

> hide sel cartoons

[Repeated 1 time(s)]

> select clear

> hide cartoons

> surface dust #3.8 size 7.77

> surface dust #3.7 size 5.84

> surface dust #3.6 size 3.21

> surface dust #3.6 size 3.19

> surface dust #3.6 size 3.17

> surface dust #3.6 size 3.15

> surface dust #3.6 size 3.13

> surface dust #3.6 size 3.11

> surface dust #3.6 size 3.09

> surface dust #3.6 size 3.07

> surface dust #3.6 size 3.05

> surface dust #3.6 size 3.03

> surface dust #3.6 size 3.01

> surface dust #3.6 size 2.96

> surface dust #3.6 size 7.49

> surface dust #3.5 size 6.9

> surface dust #3.4 size 3.21

> surface dust #3.4 size 7.41

> transparency #1#3.3-5,7#!3 50

> select clear

> select /f

8381 atoms, 8571 bonds, 2 pseudobonds, 1035 residues, 2 models selected  

> show sel cartoons

> select clear

> size stickRadius +.1

Changed 67181 bond radii  

> setattr p radius 0

Assigning radius attribute to 33 items  

> surface dust #3.3 size 3.21

> color #1#3.3-5,7#!3 byhetero

> select clear

> save C:/Users/yangx/Desktop/PhK_figures/2-Extended_Figure/beta-ADP.tif width
> 1823 height 1168 supersample 3

> save C:/Users/yangx/Desktop/PhK_figures/2-Extended_Figure/beta-ADP.cxs

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\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 0x0000021E6871A850> ->
<chimerax.map.volume.VolumeSurface object at 0x0000021E10EC5D30> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000021E10EB7F40>
'1254_global_2.9_bin_.mrc 0' -> <chimerax.map.session.GridDataState object at
0x0000021E10A3B6D0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\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 0x0000021E6871A850> -> <chimerax.map.volume.VolumeSurface object at
0x0000021E10EC5D30> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021E10EB7F40> '1254_global_2.9_bin_.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000021E10A3B6D0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x0000021E6871A850> -> <chimerax.map.volume.VolumeSurface object at
0x0000021E10EC5D30> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021E10EB7F40> '1254_global_2.9_bin_.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000021E10A3B6D0>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'1254_global_2.9_bin_.mrc 0' -> : Error while saving session data for 'models'
-> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' ->  
  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\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 0x0000021E6871A850> ->
<chimerax.map.volume.VolumeSurface object at 0x0000021E10EC5D30> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000021E10EB7F40>
'1254_global_2.9_bin_.mrc 0' -> <chimerax.map.session.GridDataState object at
0x0000021E10A3B6D0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\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 0x0000021E6871A850> -> <chimerax.map.volume.VolumeSurface object at
0x0000021E10EC5D30> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021E10EB7F40> '1254_global_2.9_bin_.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000021E10A3B6D0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x0000021E6871A850> -> <chimerax.map.volume.VolumeSurface object at
0x0000021E10EC5D30> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021E10EB7F40> '1254_global_2.9_bin_.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000021E10A3B6D0>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'1254_global_2.9_bin_.mrc 0' -> : Error while saving session data for 'models'
-> -> 'surface' -> '1254_global_2.9_bin_.mrc 0' ->  
  
File "C:\Program Files\ChimeraX\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 C:/Users/yangx/Desktop/PhK_figures/2-Extended_Figure/beta-ADP.cxs
> includeMaps true

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\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 0x0000021E6871A850> ->
<chimerax.map.volume.VolumeSurface object at 0x0000021E10EC5F10> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000021E10EBF8B0>
'1254_global_2.9_bin_.mrc 1' -> <chimerax.map.session.GridDataState object at
0x0000021E1092CC40>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\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 0x0000021E6871A850> -> <chimerax.map.volume.VolumeSurface object at
0x0000021E10EC5F10> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021E10EBF8B0> '1254_global_2.9_bin_.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x0000021E1092CC40>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x0000021E6871A850> -> <chimerax.map.volume.VolumeSurface object at
0x0000021E10EC5F10> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021E10EBF8B0> '1254_global_2.9_bin_.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x0000021E1092CC40>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'1254_global_2.9_bin_.mrc 1' -> : Error while saving session data for 'models'
-> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' ->  
  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 285, in process  
data = sm.take_snapshot(obj, session, self.state_flags)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "C:\Program Files\ChimeraX\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 0x0000021E6871A850> ->
<chimerax.map.volume.VolumeSurface object at 0x0000021E10EC5F10> 'surface' ->
<chimerax.map.volume.Volume object at 0x0000021E10EBF8B0>
'1254_global_2.9_bin_.mrc 1' -> <chimerax.map.session.GridDataState object at
0x0000021E1092CC40>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File "C:\Program Files\ChimeraX\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 0x0000021E6871A850> -> <chimerax.map.volume.VolumeSurface object at
0x0000021E10EC5F10> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021E10EBF8B0> '1254_global_2.9_bin_.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x0000021E1092CC40>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x0000021E6871A850> -> <chimerax.map.volume.VolumeSurface object at
0x0000021E10EC5F10> 'surface' -> <chimerax.map.volume.Volume object at
0x0000021E10EBF8B0> '1254_global_2.9_bin_.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x0000021E1092CC40>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'1254_global_2.9_bin_.mrc 1' -> : Error while saving session data for 'models'
-> -> 'surface' -> '1254_global_2.9_bin_.mrc 1' ->  
  
File "C:\Program Files\ChimeraX\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 496.13
OpenGL renderer: NVIDIA GeForce RTX 3060 Ti/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: ASUS
Model: System Product Name
OS: Microsoft Windows 11 专业版 (Build 22621)
Memory: 17,061,335,040
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5600X 6-Core Processor             
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2022.9.24
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5rc202211120143
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    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: 2.7.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    comtypes: 1.1.10
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.3
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.0.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.0.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.32
    psutil: 5.9.1
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2022.6
    pywin32: 303
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    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
    stack-data: 0.6.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.12
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.10.0

Change History (2)

comment:1 by pett, 3 years ago

Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → MemoryError saving session

comment:2 by Tom Goddard, 3 years ago

Resolution: → limitation
Status: assigned → closed

Ran out of memory getting a copy of map data to be saved in a session. There are lots of tools that copy map data in memory and generally we don't try to catch memory errors. The error message in the traceback MemoryError is not completely clear -- I wish it said "Out of memory". If this error happened more often I would catch it and provide that clearer message.

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