![[ChimeraX Issue Tracking System]](/trac/ChimeraX/chrome/site/ChimeraX-icon.svg){kind=icon}
Opened 14 months ago
Closed 14 months ago
#15777 closed defect (can't reproduce)
UnicodeDecodeError reading JSON file
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Input/Output | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: Windows-10-10.0.22631
ChimeraX Version: 1.6.dev202303192232 (2023-03-19 22:32:18 UTC)
Description
(Describe the actions that caused this problem to occur here)
Log:
UCSF ChimeraX version: 1.6.dev202303192232 (2023-03-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open D:\TAD\复合体.cxs format session
Log from Wed Jul 10 20:02:07 2024UCSF ChimeraX version: 1.6.dev202303192232
(2023-03-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> set bgColor #ffffff00
Log from Sun Jul 7 18:02:44 2024UCSF ChimeraX version: 1.6.dev202303192232
(2023-03-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/H352/T2 T3 AME/H352n.cxs"
Log from Sun Jul 7 16:45:51 2024UCSF ChimeraX version: 1.6.dev202303192232
(2023-03-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open "D:/H352/T2 T3 AME/H352.cxs"
Log from Wed Jun 12 11:44:57 2024UCSF ChimeraX version: 1.6.dev202303192232
(2023-03-19)
© 2016-2023 Regents of the University of California. All rights reserved.
> open D:\H352\H352.cxs format session
Log from Wed Jun 12 10:05:33 2024 Startup Messages
---
warnings | QWindowsWindow::setDarkBorderToWindow: Unable to set dark window
border.
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
notes | 2024-06-12 09:14:30,077:INFO:OpenGL_accelerate module loaded
2024-06-12 09:14:30,181:INFO:Using accelerated ArrayDatatype
UCSF ChimeraX version: 1.6.dev202303192232 (2023-03-19)
© 2016-2023 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open "D:/H352/tRNA thr T2 H240A-T3-AME.zip"
Unrecognized file suffix '.zip'
> open "D:/H352/tRNA thr T2
> H240A-T3-AME/fold_protein_rna_ion_pdb_8aw3_full_data_0.json"
fold_protein_rna_ion_pdb_8aw3_full_data_0.json does not look like Mole Online
json file, does not contain Channels.
> open "D:/H352/tRNA thr T2
> H240A-T3-AME/fold_protein_rna_ion_pdb_8aw3_model_0.cif"
Chain information for fold_protein_rna_ion_pdb_8aw3_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
Alignment identifier is 1/D
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
[Repeated 3 time(s)]
> select /D:71-72
42 atoms, 46 bonds, 2 residues, 1 model selected
> select /D
1537 atoms, 1718 bonds, 72 residues, 1 model selected
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A:1-420
3225 atoms, 3283 bonds, 420 residues, 1 model selected
> select /C:377
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C
2815 atoms, 2874 bonds, 377 residues, 1 model selected
> color sel cornflower blue
> select /C:240
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C:240
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel red
> select clear
> select
> /B:42-44,57-61,76-78,80-88,108-110,113-121,124-129,144-146,149-158,181-190,206-216,220-236,279-281,283-302,324-331,355-363
1012 atoms, 1009 bonds, 129 residues, 1 model selected
> select /B:1-2
14 atoms, 13 bonds, 2 residues, 1 model selected
> select /B:1-360
2794 atoms, 2859 bonds, 360 residues, 1 model selected
> select /B:428
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B
3334 atoms, 3418 bonds, 428 residues, 1 model selected
> color sel hot pink
> select /A:1-2
15 atoms, 14 bonds, 2 residues, 1 model selected
> select /A
5029 atoms, 5121 bonds, 652 residues, 1 model selected
> color sel forest green
> color sel orange
> ui tool show "Color Actions"
> color sel salmon
> color sel gold
> color sel sandy brown
> color sel light salmon
> color sel green yellow
> color sel blue violet
> color sel hot pink
> color sel dark violet
[Repeated 1 time(s)]
> color sel deep pink
> color sel magenta
[Repeated 1 time(s)]
> color sel dark slate blue
> color sel slate blue
> color sel sky blue
> color sel aquamarine
> color sel tan
> color sel rosy brown
> color sel tan
> color sel dark gray
> color sel pale green
> color sel dark gray
> color sel light steel blue
> color sel pale turquoise
> color sel light blue
> color sel light sky blue
> color sel aquamarine
> color sel silver
> color sel powder blue
> color sel light gray
> color sel thistle
> color sel light gray
> color sel plum
> color sel light cyan
> color sel lavender
> color sel pale goldenrod
> color sel khaki
> color sel light pink
> color sel old lace
> color sel linen
> color sel mint cream
> color sel white smoke
> color sel beige
> color sel wheat
> color sel honeydew
> color sel alice blue
> color sel khaki
> color sel moccasin
> color sel navajo white
> color sel peach puff
> color sel light pink
> color sel thistle
> color sel pale violet red
> color sel orchid
> color sel pale violet red
> color sel thistle
> color sel light gray
> color sel sky blue
> color sel pale green
> color sel dark sea green
> color sel olive drab
> color sel medium spring green
> color sel dodger blue
> color sel medium turquoise
> color sel light salmon
> color sel green
> color sel forest green
> color sel medium sea green
> color sel chocolate
> color sel brown
> color sel tomato
> color sel dark red
> color sel crimson
> color sel orange red
> color sel yellow green
> color sel slate blue
> color sel medium slate blue
> select clear
> set bgColor white
> set bgColor #ffffff00
Drag select of 1515 residues, 216 shapes
> select clear
Drag select of 1529 residues, 216 shapes
> show sel surfaces
> transparency (#!1 & sel) 70
Drag select of fold_protein_rna_ion_pdb_8aw3_model_0.cif_A SES surface, 1237
of 598108 triangles, fold_protein_rna_ion_pdb_8aw3_model_0.cif_B SES surface,
1966 of 411002 triangles, 14 residues
> select clear
Drag select of fold_protein_rna_ion_pdb_8aw3_model_0.cif_C SES surface, 559 of
443954 triangles, fold_protein_rna_ion_pdb_8aw3_model_0.cif_D SES surface, 172
of 207604 triangles, 1 shapes
> select clear
Drag select of fold_protein_rna_ion_pdb_8aw3_model_0.cif_A SES surface,
fold_protein_rna_ion_pdb_8aw3_model_0.cif_B SES surface,
fold_protein_rna_ion_pdb_8aw3_model_0.cif_C SES surface,
fold_protein_rna_ion_pdb_8aw3_model_0.cif_D SES surface, 1529 residues, 216
shapes
> hide sel surfaces
> select clear
> set bgColor black
> set bgColor transparent
Drag select of 132 residues, 23 shapes
> select clear
Drag select of 13 residues
> select clear
> select /D:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /D:32
20 atoms, 21 bonds, 1 residue, 1 model selected
> select /D:36
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /B:338
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> select /B:405
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /C:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:308
12 atoms, 12 bonds, 1 residue, 1 model selected
Drag select of 6 residues
> select clear
> select /C:240
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel yellow
> select clear
> select /D:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> show sel surfaces
> hide sel surfaces
> show sel atoms
> select clear
[Repeated 1 time(s)]
> select /D:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel hot pink
> color sel gray
> color sel orange
> color sel cyan
> color sel red
> color sel orange red
> color sel deep pink
> color sel cornflower blue
> color sel turquoise
> color sel medium turquoise
> color sel light sea green
> color sel cornflower blue
> color sel teal
> color sel medium violet red
> color sel medium slate blue
> color sel light green
> color sel yellow green
> color sel yellow
> color sel red
> color sel deep sky blue
> color sel cornflower blue
> color sel lime
> color sel lawn green
> color sel lime green
> color sel medium spring green
> color sel dark turquoise
> color sel royal blue
> color sel lime
> select /C:240
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel lime
> label (#!1 & sel) attribute name
> select /D:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> label (#!1 & sel) atoms attribute name
> label (#!1 & sel) attribute name
> label (#!1 & sel) text "{0.name} {0.number}{0.insertion_code}"
> label height 3
> label height 2.5
> save D:/H352/H352A.jpg width 2000 height 1512 supersample 3
> save D:/H352/H352A.cxs
> close session
> open "D:/H352/tRNA thr T2-T3-AME/fold_protein_rna_ion_pdb_8aw3_model_0.cif"
Chain information for fold_protein_rna_ion_pdb_8aw3_model_0.cif #1
---
Chain | Description
A | .
B | .
C | .
D | .
Alignment identifier is 1/A
Alignment identifier is 1/B
Alignment identifier is 1/C
Alignment identifier is 1/D
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
[Repeated 3 time(s)]
> select /C:376-377
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /C
2820 atoms, 2880 bonds, 377 residues, 1 model selected
> color sel hot pink
> select /B:370-428
471 atoms, 488 bonds, 59 residues, 1 model selected
> select /B
3334 atoms, 3418 bonds, 428 residues, 1 model selected
> color sel cornflower blue
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
5029 atoms, 5121 bonds, 652 residues, 1 model selected
> color sel medium slate blue
> color sel slate blue
> color sel medium purple
> select clear
> select /C:241
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C:241
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C:240
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:240
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel yellow
Drag select of 10 residues, 1 shapes
> select clear
> select /D:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel lime
> select /C:211
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /C:240
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel lime
> label sel attribute name
> select /D:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> label height 2.5
> select /C:377
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C
2820 atoms, 2880 bonds, 377 residues, 1 model selected
> color sel cornflower blue
> select /B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B
3334 atoms, 3418 bonds, 428 residues, 1 model selected
> color sel hot pink
> select clear
> select /C:240
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:240
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel lime
> select /D:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> select /D:34
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel lime
> select /C:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:239
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /C:240
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> save "D:/H352/tRNA thr T2-T3-AME/H240.jpg" width 2500 height 1501
> supersample 3
> save D:/H352/H352.cxs
——— End of log from Wed Jun 12 10:05:33 2024 ———
opened ChimeraX session
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
[Repeated 3 time(s)]
> select /C:240
10 atoms, 10 bonds, 1 residue, 1 model selected
> hbonds sel reveal true
1 hydrogen bonds found
> select /C:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel lime
> select /C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel yellow
> select /C:119
10 atoms, 10 bonds, 1 residue, 1 model selected
> select /C:119
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> color sel yellow
> select /C:210
5 atoms, 4 bonds, 1 residue, 1 model selected
> select /C:209-210
11 atoms, 10 bonds, 2 residues, 1 model selected
> select /C:206
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /C:206
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> select /C:209-210
11 atoms, 10 bonds, 2 residues, 1 model selected
> select /C:209-210
11 atoms, 10 bonds, 2 residues, 1 model selected
> select /C:203
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /C:203-204
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /C:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /C:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> show sel atoms
> select /C:121
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select /C:206
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select /C:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> show sel atoms
> ui mousemode right label
> select /C:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> label #1/C:289
> label #1/C:240
> label #1/C:209
> label #1/C:121
> label #1/C:119
> label #1/C:206
> label #1/D:34
> label height 2.5
> label #1/C:126
> ui mousemode right "move label"
> ui mousemode right translate
> ui mousemode right "move label"
> ui mousemode right translate
> save D:/H352/H352.jpg width 3000 height 1817 supersample 3
> save D:/H352/H352.cxs
——— End of log from Wed Jun 12 11:44:57 2024 ———
opened ChimeraX session
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
[Repeated 3 time(s)]
> select /B: 77,106,107,127,103,104,198,199,405,340,403,365,363/C:
> 229,227,110,111,225,108,90,121,119,206,209,221,305,306,307,308,311,312,324,319,320,321
315 atoms, 295 bonds, 35 residues, 1 model selected
> ui mousemode right label
> label delete residues
> label /B: 77,106,107,127,103,104,198,199,405,340,403,365,363/C:
> 229,227,110,111,225,108,90,121,119,206,209,221,305,306,307,308,311,312,324,319,320,321
> label height 1
> color sel lime
> save "D:/H352/T2 T3 AME/H352n.cxs"
——— End of log from Sun Jul 7 16:45:51 2024 ———
opened ChimeraX session
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
[Repeated 3 time(s)]
> select /B: 77,106,107,127,103,104,198,199,405,340,403,365,363/C:
> 229,227,110,111,225,108,90,121,119,206,209,221,305,306,307,308,311,312,324,319,320,321
315 atoms, 295 bonds, 35 residues, 1 model selected
> hbonds sel reveal true
66 hydrogen bonds found
> ui tool show "Color Actions"
> select /C:206
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> select /C:209
6 atoms, 5 bonds, 1 residue, 1 model selected
> color sel yellow
> select /C:119
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel yellow
> select /C:121
9 atoms, 8 bonds, 1 pseudobond, 1 residue, 2 models selected
> color sel yellow
> select /C:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select /C:240@CA
1 atom, 1 residue, 1 model selected
> color sel cornflower blue
> hide sel atoms
> select /C:289
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select /C:221
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /C:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> set bgColor white
> set bgColor #ffffff00
> select /B: 77,106,107,127,103,104,198,199,405,340,403,365,363/C:
> 229,227,110,111,225,108,90,121,119,206,209,221,305,306,307,308,311,312,324,319,320,321
315 atoms, 295 bonds, 11 pseudobonds, 35 residues, 2 models selected
> color sel dim gray target l
> color sel black target l
> view sel
> ui tool show "Side View"
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
> hide sel atoms
[Repeated 3 time(s)]
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> show sel cartoons
> hide sel cartoons
> select /C:240@C
1 atom, 1 residue, 1 model selected
> hide sel atoms
> hide sel cartoons
> show sel cartoons
> select /C:240
10 atoms, 10 bonds, 1 residue, 1 model selected
> hide sel atoms
> ui tool show "Side View"
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
> view
> select /A:129
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red target l
> color sel red
> select /B:123
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /B:110
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /B:138
12 atoms, 12 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /B:140
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /B:192@CA
1 atom, 1 residue, 1 model selected
> color sel medium spring green
> select clear
> select /B:192@CA
1 atom, 1 residue, 1 model selected
> color sel medium spring green
> select /B:191
11 atoms, 11 bonds, 1 residue, 1 model selected
> select /B:192
14 atoms, 15 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /D:17
23 atoms, 25 bonds, 1 residue, 1 model selected
> color sel red
Drag select of 3 residues
> select /B:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> select /B:107
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
Drag select of 1 residues
> select /B:127
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> select /B:343
10 atoms, 10 bonds, 1 residue, 1 model selected
> color sel red
> color sel medium spring green
> select /B:344
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel medium spring green
Drag select of 1 residues
> select clear
Drag select of 3 residues
> select /B:362
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:115
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:113
7 atoms, 6 bonds, 1 residue, 1 model selected
> select /C:114
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:314
11 atoms, 10 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:89
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium spring green
Drag select of 1 residues
> select /C:117
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel medium spring green
Drag select of 11 residues
> select /B:359
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:204
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:202
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:92
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:213
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:290
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:292
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:328
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:310
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:315
5 atoms, 4 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /B:194
7 atoms, 6 bonds, 1 residue, 1 model selected
> select clear
> select /B:193
7 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:309
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel medium spring green
> save "D:/H352/T2 T3 AME/H352n.cxs"
> select /C:125
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:123
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
Drag select of 2 residues
> select /C:301
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:302
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /D:35
20 atoms, 21 bonds, 1 residue, 1 model selected
> color sel red
> select /C:90
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
> select /D:36
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel red
> select /C:110@CA
1 atom, 1 residue, 1 model selected
> color sel red
> select /C:110
7 atoms, 6 bonds, 1 residue, 1 model selected
> color sel red
Drag select of 1 residues
> select /C:303
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /D:37
22 atoms, 24 bonds, 1 residue, 1 model selected
> color sel red
[Repeated 1 time(s)]
> select /C:228
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 8 residues
> select /C:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel cornflower blue
> select clear
> select /C:229@CA
1 atom, 1 residue, 1 model selected
> color sel red
> select /C:229
9 atoms, 8 bonds, 1 residue, 1 model selected
> color sel red
> select /C:227
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:230
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel medium spring green
> select /C:231
4 atoms, 3 bonds, 1 residue, 1 model selected
> color sel medium spring green
> save "D:/H352/T2 T3 AME/H352n.cxs"
——— End of log from Sun Jul 7 18:02:44 2024 ———
opened ChimeraX session
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
[Repeated 3 time(s)]
> select /A:652
6 atoms, 5 bonds, 1 residue, 1 model selected
> select /A
5029 atoms, 5121 bonds, 652 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 70
> select /B:369-428
476 atoms, 493 bonds, 60 residues, 1 model selected
> select /B
3334 atoms, 3418 bonds, 14 pseudobonds, 428 residues, 2 models selected
> show sel surfaces
> transparency (#!1 & sel) 70
> select /C:376-377
16 atoms, 15 bonds, 2 residues, 1 model selected
> select /C
2820 atoms, 2880 bonds, 38 pseudobonds, 377 residues, 2 models selected
> show sel surfaces
> transparency (#!1 & sel) 70
> select /D:72
22 atoms, 24 bonds, 1 residue, 1 model selected
> select /D
1537 atoms, 1718 bonds, 72 residues, 1 model selected
> show sel surfaces
> transparency (#!1 & sel) 70
> select /A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /A
5029 atoms, 5121 bonds, 652 residues, 1 model selected
> transparency (#!1 & sel) 60
> select /B:367-428
489 atoms, 506 bonds, 62 residues, 1 model selected
> select /B:181-428
1922 atoms, 1976 bonds, 6 pseudobonds, 248 residues, 2 models selected
> select /B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B
3334 atoms, 3418 bonds, 14 pseudobonds, 428 residues, 2 models selected
> transparency (#!1 & sel) 60
> select /C:316-377
461 atoms, 469 bonds, 2 pseudobonds, 62 residues, 2 models selected
> select /C
2820 atoms, 2880 bonds, 38 pseudobonds, 377 residues, 2 models selected
> transparency (#!1 & sel) 60
> select clear
> select /B:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:1-62
481 atoms, 489 bonds, 62 residues, 1 model selected
> select /B:202
8 atoms, 7 bonds, 1 residue, 1 model selected
> select /B:62-202
1127 atoms, 1155 bonds, 8 pseudobonds, 141 residues, 2 models selected
> ui tool show "Color Actions"
> color sel chartreuse
> color sel lawn green
> color sel lime
> color sel medium aquamarine
> color sel olive drab
> color sel medium sea green
> color sel lime green
> color sel forest green
> color sel medium sea green
> color sel medium spring green
> color sel dark turquoise
> color sel pale green
[Repeated 1 time(s)]
> color sel aquamarine
> color sel lime
> color sel turquoise
> color sel medium aquamarine
> color sel dark cyan
> color sel cornflower blue
> color sel dark cyan
> color sel light sea green
> color sel forest green
> color sel medium spring green
> color sel goldenrod
> color sel green yellow
[Repeated 1 time(s)]
> color sel goldenrod
> color sel yellow
> color sel gold
> color sel orange
> color sel sea green
> color sel medium spring green
> color sel olive drab
> color sel medium spring green
> color sel dark turquoise
> color sel turquoise
> color sel medium turquoise
> color sel light sea green
[Repeated 1 time(s)]
> color sel lime
> color sel yellow green
> ui mousemode right label
> label #1/B:68
> label delete residues
> color sel green
> color sel spring green
> label delete residues
> select clear
> label delete residues
> select /B:201-202
15 atoms, 15 bonds, 2 residues, 1 model selected
> select /B:62-202
1127 atoms, 1155 bonds, 8 pseudobonds, 141 residues, 2 models selected
> ui tool show "Color Actions"
> color sel green
> color sel lime
> color sel medium spring green
> color sel medium aquamarine
> select clear
> label #1/D:38
Drag select of fold_protein_rna_ion_pdb_8aw3_model_0.cif_C SES surface, 5728
of 435416 triangles, 5 residues
> ui mousemode right translate
> save D:/TAD/复合体结构.jpg width 4000 height 2401 supersample 3
> select clear
> save D:/TAD/复合体结构.jpg width 4000 height 2401 supersample 3
> select /D:71-72
42 atoms, 46 bonds, 2 residues, 1 model selected
> select /D
1537 atoms, 1718 bonds, 72 residues, 1 model selected
> color (#!1 & sel) light gray
> color (#!1 & sel) gray
> transparency (#!1 & sel) 60
> select clear
> save D:/TAD/复合体结构-1.jpg width 4000 height 2401 supersample 3
> save D:/TAD/复合体结构-2.jpg width 4000 height 2401 supersample 3
> save D:/TAD/复合体结构-3.jpg width 4000 height 2401 supersample 3
> save D:/TAD/复合体.cxs
——— End of log from Wed Jul 10 20:02:07 2024 ———
opened ChimeraX session
QWindowsWindow::setDarkBorderToWindow: Unable to set dark window border.
[Repeated 3 time(s)]
> close session
> open
> D:\有性特异表达\307\1-100\FG1G47150T0_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb
> format pdb
Chain information for
FG1G47150T0_unrelaxed_rank_002_alphafold2_multimer_v3_model_2_seed_000.pdb #1
---
Chain | Description
A | No description available
B | No description available
> close session
> open
> D:/TAD/识别/T3点突变/T3点突变/fold_2024_07_11_10_37_t3k198yn199h_rpl32/fold_2024_07_11_10_37_t3k198yn199h_rpl32_full_data_3.json
Traceback (most recent call last):
File "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\open_command\dialog.py",
line 162, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "E:\软件\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 "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run
result = ci.function(session, **kw_args)
File "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
119, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
File "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2897, in run
result = ci.function(session, **kw_args)
File "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
194, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
File "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
464, in collated_open
return remember_data_format()
File "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\open_command\cmd.py", line
435, in remember_data_format
models, status = func(*func_args, **func_kw)
File "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\mole\\__init__.py", line
27, in open
return mole.read_mole_json(session, data, file_name, **kw)
File "E:\软件\ChimeraX\bin\lib\site-packages\chimerax\mole\mole.py", line 38, in
read_mole_json
j = json.load(input)
File "E:\软件\ChimeraX\bin\lib\json\\__init__.py", line 293, in load
return loads(fp.read(),
File "E:\软件\ChimeraX\bin\lib\json\\__init__.py", line 341, in loads
s = s.decode(detect_encoding(s), 'surrogatepass')
File "E:\软件\ChimeraX\bin\lib\encodings\utf_32_be.py", line 11, in decode
return codecs.utf_32_be_decode(input, errors, True)
UnicodeDecodeError: 'utf-32-be' codec can't decode byte 0x00 in position
26002292: truncated data
UnicodeDecodeError: 'utf-32-be' codec can't decode byte 0x00 in position
26002292: truncated data
File "E:\软件\ChimeraX\bin\lib\encodings\utf_32_be.py", line 11, in decode
return codecs.utf_32_be_decode(input, errors, True)
See log for complete Python traceback.
OpenGL version: 3.3.0 - Build 31.0.101.4255
OpenGL renderer: Intel(R) UHD Graphics 730
OpenGL vendor: Intel
Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.2
Qt platform: windows
Manufacturer: LENOVO
Model: 90SL000RCD
OS: Microsoft Windows 11 家庭中文版 (Build 22631)
Memory: 16,881,025,024
MaxProcessMemory: 137,438,953,344
CPU: 12 12th Gen Intel(R) Core(TM) i5-12400
OSLanguage: zh-CN
Installed Packages:
alabaster: 0.7.13
appdirs: 1.4.4
asttokens: 2.2.1
Babel: 2.12.1
backcall: 0.2.0
beautifulsoup4: 4.11.2
blockdiag: 3.0.0
build: 0.10.0
certifi: 2022.12.7
cftime: 1.6.2
charset-normalizer: 3.1.0
ChimeraX-AddCharge: 1.5.9
ChimeraX-AddH: 2.2.3
ChimeraX-AlignmentAlgorithms: 2.0.1
ChimeraX-AlignmentHdrs: 3.3.1
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.9.3
ChimeraX-AlphaFold: 1.0
ChimeraX-AltlocExplorer: 1.0.3
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.43.10
ChimeraX-AtomicLibrary: 10.0.6
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.3.2
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: 2.8
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.2.2
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.3.2
ChimeraX-ChangeChains: 1.0.2
ChimeraX-CheckWaters: 1.3.1
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.2.4
ChimeraX-ColorActions: 1.0.3
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.3
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.6.dev202303192232
ChimeraX-CoreFormats: 1.1
ChimeraX-coulombic: 1.4.2
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2
ChimeraX-DistMonitor: 1.3.3
ChimeraX-DockPrep: 1.1.1
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.1.1
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: 1.1.4
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.0.12
ChimeraX-MDcrds: 2.6
ChimeraX-MedicalToolbar: 1.0.2
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.12
ChimeraX-MMTF: 2.2
ChimeraX-Modeller: 1.5.9
ChimeraX-ModelPanel: 1.3.6
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.0
ChimeraX-NRRD: 1.0
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.10.1
ChimeraX-PDB: 2.7
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-RenderByAttr: 1.1
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 3.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.1
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.8.3
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: 1.10.2
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.1.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.2.1
ChimeraX-TapeMeasure: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.1.2
ChimeraX-ToolshedUtils: 1.2.1
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.28.3
ChimeraX-uniprot: 2.2.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.1
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.1.2
comtypes: 1.1.14
contourpy: 1.0.7
cxservices: 1.2.2
cycler: 0.11.0
Cython: 0.29.33
debugpy: 1.6.6
decorator: 5.1.1
docutils: 0.19
executing: 1.2.0
filelock: 3.9.0
fonttools: 4.39.2
funcparserlib: 1.0.1
grako: 3.16.5
h5py: 3.8.0
html2text: 2020.1.16
idna: 3.4
ihm: 0.35
imagecodecs: 2022.9.26
imagesize: 1.4.1
importlib-metadata: 6.1.0
ipykernel: 6.21.1
ipython: 8.10.0
ipython-genutils: 0.2.0
ipywidgets: 8.0.4
jedi: 0.18.2
Jinja2: 3.1.2
jupyter-client: 8.0.2
jupyter-core: 5.3.0
jupyterlab-widgets: 3.0.5
kiwisolver: 1.4.4
line-profiler: 4.0.2
lxml: 4.9.2
lz4: 4.3.2
MarkupSafe: 2.1.2
matplotlib: 3.6.3
matplotlib-inline: 0.1.6
msgpack: 1.0.4
nest-asyncio: 1.5.6
netCDF4: 1.6.2
networkx: 2.8.8
nibabel: 5.0.1
nptyping: 2.5.0
numexpr: 2.8.4
numpy: 1.23.5
openvr: 1.23.701
packaging: 23.0
ParmEd: 3.4.3
parso: 0.8.3
pep517: 0.13.0
pickleshare: 0.7.5
Pillow: 9.3.0
pip: 23.0
pkginfo: 1.9.6
platformdirs: 3.1.1
prompt-toolkit: 3.0.38
psutil: 5.9.4
pure-eval: 0.2.2
pycollada: 0.7.2
pydicom: 2.3.0
Pygments: 2.14.0
pynrrd: 1.0.0
PyOpenGL: 3.1.5
PyOpenGL-accelerate: 3.1.5
pyparsing: 3.0.9
pyproject-hooks: 1.0.0
PyQt6-commercial: 6.4.2
PyQt6-Qt6: 6.4.2
PyQt6-sip: 13.4.1
PyQt6-WebEngine-commercial: 6.4.0
PyQt6-WebEngine-Qt6: 6.4.2
python-dateutil: 2.8.2
pytz: 2022.7.1
pywin32: 305
pyzmq: 25.0.1
qtconsole: 5.4.0
QtPy: 2.3.0
RandomWords: 0.4.0
requests: 2.28.2
scipy: 1.9.3
setuptools: 67.4.0
sfftk-rw: 0.7.3
six: 1.16.0
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.4
sphinx: 6.1.3
sphinx-autodoc-typehints: 1.22
sphinxcontrib-applehelp: 1.0.4
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 1.0.2
sphinxcontrib-htmlhelp: 2.0.1
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 1.0.3
sphinxcontrib-serializinghtml: 1.1.5
stack-data: 0.6.2
tables: 3.7.0
tcia-utils: 1.2.0
tifffile: 2022.10.10
tinyarray: 1.2.4
tomli: 2.0.1
tornado: 6.2
traitlets: 5.9.0
typing-extensions: 4.5.0
urllib3: 1.26.15
wcwidth: 0.2.6
webcolors: 1.12
wheel: 0.38.4
wheel-filename: 1.4.1
widgetsnbextension: 4.0.5
WMI: 1.5.1
zipp: 3.15.0
Change History (2)
comment:1 by , 14 months ago
| Component: | Unassigned → Input/Output |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → UnicodeDecodeError reading JSON file |
comment:2 by , 14 months ago
| Resolution: | → can't reproduce |
|---|---|
| Status: | accepted → closed |
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