Opened 2 years ago

Closed 2 years ago

#8928 closed defect (limitation)

MemoryError saving maps in sessions

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-10-10.0.19043
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "C:\\\Users\\\Administrator\\\Desktop\\\To PP\\\To
> PP\\\J377\\\J377-Crt8mer-0415.mrc"

Opened J377-Crt8mer-0415.mrc as #1, grid size 432,432,432, pixel 1.11, shown
at level 0.0381, step 2, values float32  

> open "D:/微信下载文件/WeChat
> Files/wxid_2n1dull1jbk622/FileStorage/File/2023-05/Crt-8-0501-coot-0.pdb"

Chain information for Crt-8-0501-coot-0.pdb #2  
---  
Chain | Description  
A I | No description available  
B J | No description available  
C M | No description available  
D N | No description available  
E G K O | No description available  
F L | No description available  
H P | No description available  
  

> open "D:/微信下载文件/WeChat
> Files/wxid_2n1dull1jbk622/FileStorage/File/2023-05/Crt-8-0501-coot-0.pdb"

Chain information for Crt-8-0501-coot-0.pdb #3  
---  
Chain | Description  
A I | No description available  
B J | No description available  
C M | No description available  
D N | No description available  
E G K O | No description available  
F L | No description available  
H P | No description available  
  

> close #3

> volume #1 step 1

> volume #1 level 0.1

> surface dust #1 size 11.1

> hide atoms

> volume #1 level 0.3256

> close #2

> open "D:/微信下载文件/WeChat
> Files/wxid_2n1dull1jbk622/FileStorage/File/2023-05/Crt-8-0501-coot-0.pdb"

Chain information for Crt-8-0501-coot-0.pdb #2  
---  
Chain | Description  
A I | No description available  
B J | No description available  
C M | No description available  
D N | No description available  
E G K O | No description available  
F L | No description available  
H P | No description available  
  

> volume #1 level 0.1

> hide atoms

> volume #1 level 0.2215

> hide #2 models

> show #2 models

> color #2 #3b6691ff

> color bfactor

31984 atoms, 3648 residues, atom bfactor range 20 to 374  

> set bgColor white

> set bgColor #ffffff00

> close #2

> open "D:/微信下载文件/WeChat
> Files/wxid_2n1dull1jbk622/FileStorage/File/2023-05/Crt-8-0501-coot-0.pdb"

Chain information for Crt-8-0501-coot-0.pdb #2  
---  
Chain | Description  
A I | No description available  
B J | No description available  
C M | No description available  
D N | No description available  
E G K O | No description available  
F L | No description available  
H P | No description available  
  

> show cartoons

> hide atoms

> volume #1 level 0.1

> ui tool show "Show Sequence Viewer"

> split #2

Split Crt-8-0501-coot-0.pdb (#2) into 16 models  
Chain information for Crt-8-0501-coot-0.pdb A #2.1  
---  
Chain | Description  
A | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb B #2.2  
---  
Chain | Description  
B | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb C #2.3  
---  
Chain | Description  
C | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb D #2.4  
---  
Chain | Description  
D | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb E #2.5  
---  
Chain | Description  
E | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb F #2.6  
---  
Chain | Description  
F | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb G #2.7  
---  
Chain | Description  
G | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb H #2.8  
---  
Chain | Description  
H | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb I #2.9  
---  
Chain | Description  
I | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb J #2.10  
---  
Chain | Description  
J | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb K #2.11  
---  
Chain | Description  
K | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb L #2.12  
---  
Chain | Description  
L | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb M #2.13  
---  
Chain | Description  
M | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb N #2.14  
---  
Chain | Description  
N | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb O #2.15  
---  
Chain | Description  
O | No description available  
  
Chain information for Crt-8-0501-coot-0.pdb P #2.16  
---  
Chain | Description  
P | No description available  
  

> hide #!1 models

> select add #2.1

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> select subtract #2.1

Nothing selected  

> select add #2.1

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> select subtract #2.1

Nothing selected  

> select add #2.1

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium blue

> select add #2.2

7147 atoms, 7328 bonds, 870 residues, 2 models selected  

> select subtract #2.2

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> select add #2.4

7150 atoms, 7331 bonds, 870 residues, 2 models selected  

> select subtract #2.4

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> select add #2.5

4040 atoms, 4182 bonds, 469 residues, 2 models selected  

> select subtract #2.5

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> select add #2.5

4040 atoms, 4182 bonds, 469 residues, 2 models selected  

> color sel yellow

> undo

> select subtract #2.1

422 atoms, 472 bonds, 21 residues, 1 model selected  

> select add #2

31984 atoms, 33114 bonds, 3648 residues, 17 models selected  

> select subtract #2

Nothing selected  

> select add #2.6

432 atoms, 485 bonds, 21 residues, 1 model selected  

> color sel yellow

> select subtract #2.6

Nothing selected  

> select add #2.7

422 atoms, 472 bonds, 21 residues, 1 model selected  

> select subtract #2.7

Nothing selected  

> select add #2.7

422 atoms, 472 bonds, 21 residues, 1 model selected  

> color sel yellow

> select subtract #2.7

Nothing selected  

> select add #2.8

411 atoms, 461 bonds, 20 residues, 1 model selected  

> color sel orange red

[Repeated 1 time(s)]

> select subtract #2.8

Nothing selected  

> select add #2.9

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> select subtract #2.9

Nothing selected  

> select add #2.9

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> select subtract #2.9

Nothing selected  

> select add #2.6

432 atoms, 485 bonds, 21 residues, 1 model selected  

> select add #2.7

854 atoms, 957 bonds, 42 residues, 2 models selected  

> select add #2.8

1265 atoms, 1418 bonds, 62 residues, 3 models selected  

> select add #2.5

1687 atoms, 1890 bonds, 83 residues, 4 models selected  

> select subtract #2.6

1255 atoms, 1405 bonds, 62 residues, 3 models selected  

> select subtract #2.7

833 atoms, 933 bonds, 41 residues, 2 models selected  

> select subtract #2.8

422 atoms, 472 bonds, 21 residues, 1 model selected  

> color sel orange red

> select add #2.6

854 atoms, 957 bonds, 42 residues, 2 models selected  

> select add #2.7

1276 atoms, 1429 bonds, 63 residues, 3 models selected  

> select add #2.8

1687 atoms, 1890 bonds, 83 residues, 4 models selected  

> show sel atoms

> nucleotides sel stubs

> select subtract #2.8

1276 atoms, 1429 bonds, 63 residues, 3 models selected  

> select subtract #2.7

854 atoms, 957 bonds, 42 residues, 2 models selected  

> select subtract #2.6

422 atoms, 472 bonds, 21 residues, 1 model selected  

> select subtract #2.5

Nothing selected  

> select add #2.9

3618 atoms, 3710 bonds, 448 residues, 1 model selected  

> color sel dodger blue

> select subtract #2.9

Nothing selected  

> select add #2.10

3529 atoms, 3618 bonds, 422 residues, 1 model selected  

> select subtract #2.10

Nothing selected  

> select add #2.10

3529 atoms, 3618 bonds, 422 residues, 1 model selected  

> color sel medium orchid

> select subtract #2.10

Nothing selected  

> select add #2.11

422 atoms, 472 bonds, 21 residues, 1 model selected  

> select subtract #2.11

Nothing selected  

> select add #2.11

422 atoms, 472 bonds, 21 residues, 1 model selected  

> color sel yellow

> color sel orange red

> select subtract #2.11

Nothing selected  

> select add #2.12

432 atoms, 485 bonds, 21 residues, 1 model selected  

> color sel yellow

> select subtract #2.12

Nothing selected  

> select add #2.13

3626 atoms, 3718 bonds, 449 residues, 1 model selected  

> select subtract #2.13

Nothing selected  

> select add #2.13

3626 atoms, 3718 bonds, 449 residues, 1 model selected  

> color sel medium blue

> select subtract #2.13

Nothing selected  

> select add #2.14

3532 atoms, 3621 bonds, 422 residues, 1 model selected  

> color sel rebecca purple

> select subtract #2.14

Nothing selected  

> select add #2.15

422 atoms, 472 bonds, 21 residues, 1 model selected  

> color sel yellow

> select subtract #2.15

Nothing selected  

> select add #2.16

411 atoms, 461 bonds, 20 residues, 1 model selected  

> color sel orange red

> select subtract #2.16

Nothing selected  

> select add #2.3

3626 atoms, 3718 bonds, 449 residues, 1 model selected  

> select subtract #2.3

Nothing selected  

> select add #2.4

3532 atoms, 3621 bonds, 422 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel medium orchid

> select subtract #2.4

Nothing selected  

> select add #2.2

3529 atoms, 3618 bonds, 422 residues, 1 model selected  

> color sel rebecca purple

> select add #2

31984 atoms, 33114 bonds, 3648 residues, 17 models selected  

> select subtract #2

Nothing selected  

> ui tool show "Show Sequence Viewer"

> sequence chain #2.2/B #2.10/J

Alignment identifier is 1  

> sequence chain #2.4/D #2.14/N

Alignment identifier is 2  

> select #2.2/B:1-2 #2.10/J:1-2

38 atoms, 36 bonds, 4 residues, 2 models selected  

> select #2.2/B:1-129 #2.10/J:1-129

2100 atoms, 2140 bonds, 258 residues, 2 models selected  
1 [ID: 1] region chains B,J [1-129] RMSD: 39.787  
  

> select #2.4/D:1-2 #2.14/N:1-2

38 atoms, 36 bonds, 4 residues, 2 models selected  

> select #2.4/D:1-67 #2.14/N:1-67

1108 atoms, 1134 bonds, 134 residues, 2 models selected  
2 [ID: 2] region chains D,N [1-67] RMSD: 43.654  
  

> select #2.4/D:1-2 #2.14/N:1-2

38 atoms, 36 bonds, 4 residues, 2 models selected  

> select #2.4/D:1-90 #2.14/N:1-90

1466 atoms, 1494 bonds, 180 residues, 2 models selected  
2 [ID: 2] region chains D,N [1-90] RMSD: 40.159  
  

> ui mousemode right select

> select clear

> select #2.4/D:1

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

> select add #2.4/D:163

17 atoms, 15 bonds, 2 residues, 1 model selected  

> select up

218 atoms, 221 bonds, 26 residues, 1 model selected  

> select clear

> select #2.4/D:1

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

> select up

142 atoms, 145 bonds, 17 residues, 1 model selected  

> select add #2.4/D:18

149 atoms, 151 bonds, 18 residues, 1 model selected  

> select up

226 atoms, 231 bonds, 27 residues, 1 model selected  

> select add #2.4/D:28

234 atoms, 238 bonds, 28 residues, 1 model selected  

> select up

390 atoms, 402 bonds, 46 residues, 1 model selected  

> select add #2.4/D:47

396 atoms, 407 bonds, 47 residues, 1 model selected  

> select up

466 atoms, 478 bonds, 55 residues, 1 model selected  

> select up

3532 atoms, 3621 bonds, 422 residues, 1 model selected  

> select down

466 atoms, 478 bonds, 55 residues, 1 model selected  

> select add #2.4/D:56

474 atoms, 485 bonds, 56 residues, 1 model selected  

> select up

586 atoms, 599 bonds, 71 residues, 1 model selected  

> select clear

> select #2.4/D:1 #2.14/N:1

16 atoms, 14 bonds, 2 residues, 2 models selected  

> select #2.4/D:1-163 #2.14/N:1-163

2672 atoms, 2728 bonds, 326 residues, 2 models selected  
2 [ID: 2] region chains D,N [1-163] RMSD: 46.050  
  

> color sel forest green

> select #2.2/B:163 #2.10/J:163

18 atoms, 16 bonds, 2 residues, 2 models selected  

> select #2.2/B:1-163 #2.10/J:1-163

2670 atoms, 2726 bonds, 326 residues, 2 models selected  
1 [ID: 1] region chains B,J [1-163] RMSD: 47.192  
  

> ui tool show "Color Actions"

> color sel dark green

[Repeated 1 time(s)]

> select clear

> select #2.14/N:1

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

> select up

131 atoms, 133 bonds, 16 residues, 1 model selected  

> select add #2.14/N:17

142 atoms, 144 bonds, 17 residues, 1 model selected  

> select up

226 atoms, 231 bonds, 27 residues, 1 model selected  

> select add #2.14/N:28

234 atoms, 238 bonds, 28 residues, 1 model selected  

> select up

390 atoms, 402 bonds, 46 residues, 1 model selected  

> select add #2.14/N:47

396 atoms, 407 bonds, 47 residues, 1 model selected  

> select up

466 atoms, 478 bonds, 55 residues, 1 model selected  

> select add #2.14/N:56

474 atoms, 485 bonds, 56 residues, 1 model selected  

> select up

586 atoms, 599 bonds, 71 residues, 1 model selected  

> select add #2.14/N:72

595 atoms, 607 bonds, 72 residues, 1 model selected  

> select up

716 atoms, 730 bonds, 88 residues, 1 model selected  

> select add #2.14/N:89

725 atoms, 738 bonds, 89 residues, 1 model selected  

> select up

887 atoms, 904 bonds, 109 residues, 1 model selected  

> select add #2.14/N:110

895 atoms, 911 bonds, 110 residues, 1 model selected  

> select up

912 atoms, 929 bonds, 112 residues, 1 model selected  

> select add #2.14/N:115

920 atoms, 936 bonds, 113 residues, 1 model selected  

> select subtract #2.14/N:105

908 atoms, 922 bonds, 112 residues, 1 model selected  

> select add #2.14/N:113

915 atoms, 928 bonds, 113 residues, 1 model selected  

> select add #2.14/N:114

926 atoms, 938 bonds, 114 residues, 1 model selected  

> select add #2.14/N:105

938 atoms, 950 bonds, 115 residues, 1 model selected  

> select add #2.14/N:116

946 atoms, 957 bonds, 116 residues, 1 model selected  

> select up

1002 atoms, 1020 bonds, 123 residues, 1 model selected  

> select add #2.14/N:124

1016 atoms, 1035 bonds, 124 residues, 1 model selected  

> select up

1117 atoms, 1138 bonds, 137 residues, 1 model selected  

> select add #2.14/N:138

1126 atoms, 1146 bonds, 138 residues, 1 model selected  

> select up

1188 atoms, 1212 bonds, 146 residues, 1 model selected  

> select add #2.14/N:147

1198 atoms, 1222 bonds, 147 residues, 1 model selected  

> select up

1281 atoms, 1307 bonds, 157 residues, 1 model selected  

> select add #2.14/N:158

1292 atoms, 1318 bonds, 158 residues, 1 model selected  

> select up

1376 atoms, 1404 bonds, 168 residues, 1 model selected  

> select add #2.14/N:369

1390 atoms, 1419 bonds, 169 residues, 1 model selected  

> select subtract #2.14/N:369

1376 atoms, 1404 bonds, 168 residues, 1 model selected  

> select subtract #2.14/N:168

1367 atoms, 1395 bonds, 167 residues, 1 model selected  

> select subtract #2.14/N:167

1358 atoms, 1386 bonds, 166 residues, 1 model selected  

> select subtract #2.14/N:166

1349 atoms, 1377 bonds, 165 residues, 1 model selected  

> select subtract #2.14/N:165

1341 atoms, 1369 bonds, 164 residues, 1 model selected  

> select subtract #2.14/N:164

1336 atoms, 1364 bonds, 163 residues, 1 model selected  

> ui tool show "Color Actions"

> color sel dark green

> select clear

> select #2.10/J:1

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

> select up

123 atoms, 125 bonds, 15 residues, 1 model selected  

> select add #2.10/J:16

131 atoms, 132 bonds, 16 residues, 1 model selected  

> select up

233 atoms, 238 bonds, 28 residues, 1 model selected  

> select add #2.10/J:29

237 atoms, 241 bonds, 29 residues, 1 model selected  

> select up

309 atoms, 317 bonds, 37 residues, 1 model selected  

> select add #2.10/J:38

320 atoms, 328 bonds, 38 residues, 1 model selected  

> select up

336 atoms, 345 bonds, 40 residues, 1 model selected  

> select add #2.10/J:41

345 atoms, 353 bonds, 41 residues, 1 model selected  

> select up

364 atoms, 373 bonds, 44 residues, 1 model selected  

> select add #2.10/J:45

375 atoms, 384 bonds, 45 residues, 1 model selected  

> select up

465 atoms, 477 bonds, 55 residues, 1 model selected  

> select add #2.10/J:56

473 atoms, 484 bonds, 56 residues, 1 model selected  

> select up

548 atoms, 561 bonds, 66 residues, 1 model selected  

> select add #2.10/J:67

553 atoms, 565 bonds, 67 residues, 1 model selected  

> select up

574 atoms, 587 bonds, 70 residues, 1 model selected  

> select add #2.10/J:71

585 atoms, 597 bonds, 71 residues, 1 model selected  

> select up

3529 atoms, 3618 bonds, 422 residues, 1 model selected  

> select down

585 atoms, 597 bonds, 71 residues, 1 model selected  

> select add #2.10/J:72

594 atoms, 605 bonds, 72 residues, 1 model selected  

> select up

715 atoms, 729 bonds, 88 residues, 1 model selected  

> select add #2.10/J:89

724 atoms, 737 bonds, 89 residues, 1 model selected  

> select up

842 atoms, 858 bonds, 104 residues, 1 model selected  

> select add #2.10/J:105

854 atoms, 870 bonds, 105 residues, 1 model selected  

> select up

870 atoms, 887 bonds, 107 residues, 1 model selected  

> select add #2.10/J:108

878 atoms, 894 bonds, 108 residues, 1 model selected  

> select up

1015 atoms, 1035 bonds, 124 residues, 1 model selected  

> select add #2.10/J:125

1020 atoms, 1039 bonds, 125 residues, 1 model selected  

> select up

1125 atoms, 1146 bonds, 138 residues, 1 model selected  

> select add #2.10/J:139

1133 atoms, 1153 bonds, 139 residues, 1 model selected  

> select up

1218 atoms, 1243 bonds, 150 residues, 1 model selected  

> select #2.10/J:151

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

> select clear

Drag select of 135 residues  
Drag select of 39 residues  
Drag select of 9 residues  
Drag select of 2 residues  
Drag select of 3 residues  

> select add #2.10/J:43

1256 atoms, 6 bonds, 153 residues, 3 models selected  

> select #2.10/J:10

5 atoms, 4 bonds, 1 residue, 1 model selected  
Drag select of 104 residues  
Drag select of 64 residues  
Drag select of 6 residues  

> select subtract #2.2/B:108

1246 atoms, 4 bonds, 152 residues, 2 models selected  

> select add #2.10/J:68

1250 atoms, 7 bonds, 153 residues, 2 models selected  

> select add #2.10/J:103

1258 atoms, 14 bonds, 154 residues, 2 models selected  

> select add #2.10/J:118

1266 atoms, 21 bonds, 155 residues, 2 models selected  

> select add #2.10/J:137

1275 atoms, 29 bonds, 156 residues, 2 models selected  

> select add #2.10/J:10

1280 atoms, 29 bonds, 157 residues, 2 models selected  

> select subtract #2.14/N:117

1275 atoms, 29 bonds, 156 residues, 2 models selected  

> select subtract #2.14/N:118

1267 atoms, 29 bonds, 155 residues, 1 model selected  

> select add #2.10/J:52

1276 atoms, 37 bonds, 156 residues, 1 model selected  

> select add #2.10/J:148

1282 atoms, 42 bonds, 157 residues, 1 model selected  

> select add #2.10/J:155

1291 atoms, 50 bonds, 158 residues, 1 model selected  

> select add #2.10/J:159

1299 atoms, 57 bonds, 159 residues, 1 model selected  

> select add #2.10/J:160

1309 atoms, 67 bonds, 160 residues, 1 model selected  

> select add #2.10/J:161

1317 atoms, 74 bonds, 161 residues, 1 model selected  

> select add #2.10/J:162

1326 atoms, 82 bonds, 162 residues, 1 model selected  

> select add #2.10/J:163

1335 atoms, 90 bonds, 163 residues, 1 model selected  

> color sel forest green

> select clear

> ui tool show "Color Zone"

> color zone #1 near #2.1 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #3.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #3.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

QWindowsWindow::setGeometry: Unable to set geometry 1920x1193+0+35 (frame:
1942x1249-11-10) on QWidgetWindow/"MainWindowClassWindow" on "\\\\.\DISPLAY1".
Resulting geometry: 1920x1046+0+34 (frame: 1942x1102-11-11) margins: 11, 45,
11, 11 minimum size: 506x795 MINMAXINFO(maxSize=POINT(x=0, y=0),
maxpos=POINT(x=0, y=0), maxtrack=POINT(x=0, y=0), mintrack=POINT(x=781,
y=1249)))  

> color zone #1 near #2.2 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #4.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #4.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 2 as #4.3, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.3 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #5.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #5.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.4 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #6.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #6.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 2 as #6.3, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.5 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #7.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #7.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.6 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #8.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #8.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.7 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #9.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #9.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.8 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #10.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #10.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> hide #2.2 models

> show #2.2 models

> hide #!4.1 models

> hide #!5 models

> hide #!6 models

> show #!6 models

> show #!5 models

> show #!4.1 models

> hide #!3.1 models

> hide #!4.1 models

> hide #!5.1 models

> hide #!6.1 models

> hide #!7.1 models

> hide #!8 models

> show #!8 models

> hide #!8 models

> hide #!9.1 models

> show #!8 models

> hide #!8.1 models

> hide #!10.1 models

> color zone #1 near #2.9 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #11.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #11.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.10 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #12.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #12.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 2 as #12.3, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.11 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #13.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #13.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.13 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #14.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #14.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.14 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #15.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #15.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 2 as #15.3, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.15 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #16.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #16.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> color zone #1 near #2.16 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #17.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #17.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> hide #!17.1 models

> hide #!16.1 models

> hide #!15.1 models

> hide #!14.1 models

> hide #!13.1 models

> hide #!12.1 models

> hide #!11.1 models

> color #3.2 #5fa2e9ff models

> color #3.2 #3b6691ff models

> color #3.2 #5fa2e9ff models

> color #4.2 #7e99b8ff models

> color #4.2 #65905bff models

> color #4.3 #b05aadff models

> color #4.3 #785cabff models

> color #5.2 #5fa2e9ff models

> color #5.2 #7e99b8ff models

> color #6.2 #65905bff models

> color #6.2 darkseagreen models

> color #6.3 #b05aadff models

> color #6.3 #774879ff models

> color #6.3 #b05aadff models

> color #11.2 #3b6691ff models

> color #11.2 #7e99b8ff models

> color #12.2 #65905bff models

> color #12.2 darkseagreen models

> color #12.3 #65905bff models

> color #12.3 #785cabff models

> color #12.3 #b05aadff models

[Repeated 1 time(s)]

> color #14.2 #5fa2e9ff models

> color #15.2 #65905bff models

> color #15.2 #774879ff models

> color #15.2 #36600eff models

> color #15.2 #65905bff models

> color #15.2 #36600eff models

> lighting soft

> lighting shadows true intensity 0.5

> select #2.12/L:21

20 atoms, 21 bonds, 1 residue, 1 model selected  

> select up

432 atoms, 485 bonds, 21 residues, 1 model selected  

> select up

31984 atoms, 33114 bonds, 3648 residues, 16 models selected  

> select down

432 atoms, 485 bonds, 21 residues, 1 model selected  

> ui tool show "Color Zone"

> color zone #1 near #2.12 distance 2

> volume splitbyzone #1

Opened J377-Crt8mer-0415.mrc 0 as #18.1, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  
Opened J377-Crt8mer-0415.mrc 1 as #18.2, grid size 432,432,432, pixel 1.11,
shown at level 0.1, step 1, values float32  

> hide #!18.1 models

> save "C:/Users/Administrator/Desktop/To PP/To PP/J377/J377.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 0x00000148EE2FC940> ->
<chimerax.map.volume.VolumeSurface object at 0x0000014895697430> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000148955686D0>
'J377-Crt8mer-0415.mrc 0' -> <chimerax.map.session.GridDataState object at
0x0000014899D3A670>  
  
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 0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697430> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148955686D0> 'J377-Crt8mer-0415.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000014899D3A670>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697430> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148955686D0> 'J377-Crt8mer-0415.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000014899D3A670>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J377-Crt8mer-0415.mrc 0' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'J377-Crt8mer-0415.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 0x00000148EE2FC940> ->
<chimerax.map.volume.VolumeSurface object at 0x0000014895697430> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000148955686D0>
'J377-Crt8mer-0415.mrc 0' -> <chimerax.map.session.GridDataState object at
0x0000014899D3A670>  
  
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 0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697430> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148955686D0> 'J377-Crt8mer-0415.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000014899D3A670>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697430> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148955686D0> 'J377-Crt8mer-0415.mrc 0' ->
<chimerax.map.session.GridDataState object at 0x0000014899D3A670>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J377-Crt8mer-0415.mrc 0' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'J377-Crt8mer-0415.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.  
  

> color #15.2 #65905bff models

> color #4.2 #36600eff models

> color #4.2 #65905bff models

> select add #2

31984 atoms, 33114 bonds, 3648 residues, 17 models selected  

> select subtract #2

Nothing selected  

> select add #2

31984 atoms, 33114 bonds, 3648 residues, 17 models selected  

> select subtract #2

Nothing selected  

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> select add #1

2 models selected  

> select subtract #1

Nothing selected  

> save "C:/Users/Administrator/Desktop/To PP/To PP/J377/J377.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 0x00000148EE2FC940> ->
<chimerax.map.volume.VolumeSurface object at 0x0000014895697640> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000148956970D0>
'J377-Crt8mer-0415.mrc 1' -> <chimerax.map.session.GridDataState object at
0x00000148A3CCB490>  
  
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 0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148A3CCB490>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148A3CCB490>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J377-Crt8mer-0415.mrc 1' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'J377-Crt8mer-0415.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 0x00000148EE2FC940> ->
<chimerax.map.volume.VolumeSurface object at 0x0000014895697640> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000148956970D0>
'J377-Crt8mer-0415.mrc 1' -> <chimerax.map.session.GridDataState object at
0x00000148A3CCB490>  
  
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 0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148A3CCB490>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148A3CCB490>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J377-Crt8mer-0415.mrc 1' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'J377-Crt8mer-0415.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.  
  

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> show #!2 models

> hide #!2 models

> hide #2.1 models

> hide #2.2 models

> hide #2.3 models

> hide #2.4 models

> hide #2.5 models

> hide #2.6 models

> hide #2.7 models

> hide #2.8 models

> hide #2.9 models

> hide #2.10 models

> hide #2.11 models

> hide #2.12 models

> hide #2.13 models

> hide #2.14 models

> hide #2.15 models

> hide #2.16 models

> save "C:/Users/Administrator/Desktop/To PP/To PP/J377/J377.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 0x00000148EE2FC940> ->
<chimerax.map.volume.VolumeSurface object at 0x0000014895697640> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000148956970D0>
'J377-Crt8mer-0415.mrc 1' -> <chimerax.map.session.GridDataState object at
0x00000148AF6DF7F0>  
  
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 0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148AF6DF7F0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148AF6DF7F0>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J377-Crt8mer-0415.mrc 1' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'J377-Crt8mer-0415.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 0x00000148EE2FC940> ->
<chimerax.map.volume.VolumeSurface object at 0x0000014895697640> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000148956970D0>
'J377-Crt8mer-0415.mrc 1' -> <chimerax.map.session.GridDataState object at
0x00000148AF6DF7F0>  
  
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 0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148AF6DF7F0>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148AF6DF7F0>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J377-Crt8mer-0415.mrc 1' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'J377-Crt8mer-0415.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.  
  

> save "C:/Users/Administrator/Desktop/To PP/To PP/J377/1.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 0x00000148EE2FC940> ->
<chimerax.map.volume.VolumeSurface object at 0x0000014895697640> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000148956970D0>
'J377-Crt8mer-0415.mrc 1' -> <chimerax.map.session.GridDataState object at
0x00000148C94E2A90>  
  
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 0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148C94E2A90>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148C94E2A90>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J377-Crt8mer-0415.mrc 1' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'J377-Crt8mer-0415.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 0x00000148EE2FC940> ->
<chimerax.map.volume.VolumeSurface object at 0x0000014895697640> 'surface' ->
<chimerax.map.volume.Volume object at 0x00000148956970D0>
'J377-Crt8mer-0415.mrc 1' -> <chimerax.map.session.GridDataState object at
0x00000148C94E2A90>  
  
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 0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148C94E2A90>: Error while
saving session data for 'models' -> <chimerax.core.models.Models object at
0x00000148EE2FC940> -> <chimerax.map.volume.VolumeSurface object at
0x0000014895697640> 'surface' -> <chimerax.map.volume.Volume object at
0x00000148956970D0> 'J377-Crt8mer-0415.mrc 1' ->
<chimerax.map.session.GridDataState object at 0x00000148C94E2A90>  
  
ValueError: error processing: 'models' -> -> 'surface' ->
'J377-Crt8mer-0415.mrc 1' -> : Error while saving session data for 'models' ->
-> 'surface' -> 'J377-Crt8mer-0415.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: 3.3.14802 Core Profile Forward-Compatible Context 21.12.1 30.0.14011.3017
OpenGL renderer: AMD Radeon(TM) Graphics
OpenGL vendor: ATI Technologies Inc.

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: Dell Inc.
Model: Inspiron 5415
OS: Microsoft Windows 10 专业版 (Build 19043)
Memory: 16,483,872,768
MaxProcessMemory: 137,438,953,344
CPU: 12 AMD Ryzen 5 5500U with Radeon Graphics         
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: 1.5
    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: 1.6.4
    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: 5.1.0
    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: 5.1.0
    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: 3.0.33
    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: 0.6.2
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    WMI: 1.5.1
    zipp: 3.11.0

Change History (2)

comment:1 by pett, 2 years ago

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

comment:2 by Tom Goddard, 2 years ago

Resolution: → limitation
Status: assigned → closed

User created about 30 large maps 432 by 432 by 432 (float), 0.3 GB each, so about 10 GBytes using split by color then tried to save them with option "includeMaps true". That ran out of memory on this 16 GB Windows machine.

Could report a clearer error message. The numpy array.tobytes() method is giving MemoryError and would be clearer if it said "Out of Memory". But this is such a rare situation I don't think I will add better error messages unless it is reported more often. I think it has been reported once before possibly by the same user.

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