Opened 4 years ago

Closed 4 years ago

#5530 closed defect (duplicate)

Write GLTF: index 1 is out of bounds for axis 0 with size 1

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
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-10-10.0.19041
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 3dkt

3dkt title:  
Crystal structure of Thermotoga maritima encapsulin [more info...]  
  
Chain information for 3dkt #1  
---  
Chain | Description  
A B C D E F G H I J | Maritimacin  
K L M N O P Q R S T | Putative uncharacterized protein  
  
3dkt mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sym #1 assembly 1

> view

> show #2 surfaces

> select /K:106-113

112 atoms, 110 bonds, 16 residues, 2 models selected  

> hide #!2 models

> show #!2 models

> save "C:/Users/nuren/OneDrive - The University of Sydney (Staff)/Cover
> image-ChemSysChem/shell.x3d"

> preset "overall look" publication

Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t

  

> select #2.20

56 atoms, 8 residues, 1 model selected  

> select #2.19

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 20

> select clear

Drag select of 3dkt assembly 1_A SES surface, 3dkt assembly 1_A SES surface,
3dkt assembly 1_A SES surface, 3dkt assembly 1_A SES surface, 3dkt assembly
1_A SES surface, 3dkt assembly 1_A SES surface, 3dkt assembly 1_B SES surface,
3dkt assembly 1_B SES surface, 3dkt assembly 1_B SES surface, 3dkt assembly
1_B SES surface, 3dkt assembly 1_B SES surface, 3dkt assembly 1_B SES surface,
3dkt assembly 1_C SES surface, 3dkt assembly 1_C SES surface, 3dkt assembly
1_C SES surface, 3dkt assembly 1_C SES surface, 3dkt assembly 1_C SES surface,
3dkt assembly 1_C SES surface, 3dkt assembly 1_D SES surface, 3dkt assembly
1_D SES surface, 3dkt assembly 1_D SES surface, 3dkt assembly 1_D SES surface,
3dkt assembly 1_D SES surface, 3dkt assembly 1_D SES surface, 3dkt assembly
1_E SES surface, 3dkt assembly 1_E SES surface, 3dkt assembly 1_E SES surface,
3dkt assembly 1_E SES surface, 3dkt assembly 1_E SES surface, 3dkt assembly
1_E SES surface, 3dkt assembly 1_F SES surface, 3dkt assembly 1_F SES surface,
3dkt assembly 1_F SES surface, 3dkt assembly 1_F SES surface, 3dkt assembly
1_F SES surface, 3dkt assembly 1_F SES surface, 3dkt assembly 1_G SES surface,
3dkt assembly 1_G SES surface, 3dkt assembly 1_G SES surface, 3dkt assembly
1_G SES surface, 3dkt assembly 1_G SES surface, 3dkt assembly 1_G SES surface,
3dkt assembly 1_H SES surface, 3dkt assembly 1_H SES surface, 3dkt assembly
1_H SES surface, 3dkt assembly 1_H SES surface, 3dkt assembly 1_H SES surface,
3dkt assembly 1_H SES surface, 3dkt assembly 1_I SES surface, 3dkt assembly
1_I SES surface, 3dkt assembly 1_I SES surface, 3dkt assembly 1_I SES surface,
3dkt assembly 1_I SES surface, 3dkt assembly 1_I SES surface, 3dkt assembly
1_J SES surface, 3dkt assembly 1_J SES surface, 3dkt assembly 1_J SES surface,
3dkt assembly 1_J SES surface, 3dkt assembly 1_J SES surface, 3dkt assembly
1_J SES surface, 3dkt assembly 1_K SES surface, 3dkt assembly 1_K SES surface,
3dkt assembly 1_K SES surface, 3dkt assembly 1_K SES surface, 3dkt assembly
1_K SES surface, 3dkt assembly 1_K SES surface, 3dkt assembly 1_L SES surface,
3dkt assembly 1_L SES surface, 3dkt assembly 1_L SES surface, 3dkt assembly
1_L SES surface, 3dkt assembly 1_L SES surface, 3dkt assembly 1_L SES surface,
3dkt assembly 1_M SES surface, 3dkt assembly 1_M SES surface, 3dkt assembly
1_M SES surface, 3dkt assembly 1_M SES surface, 3dkt assembly 1_M SES surface,
3dkt assembly 1_M SES surface, 3dkt assembly 1_N SES surface, 3dkt assembly
1_N SES surface, 3dkt assembly 1_N SES surface, 3dkt assembly 1_N SES surface,
3dkt assembly 1_N SES surface, 3dkt assembly 1_N SES surface, 3dkt assembly
1_O SES surface, 3dkt assembly 1_O SES surface, 3dkt assembly 1_O SES surface,
3dkt assembly 1_O SES surface, 3dkt assembly 1_O SES surface, 3dkt assembly
1_O SES surface, 3dkt assembly 1_P SES surface, 3dkt assembly 1_P SES surface,
3dkt assembly 1_P SES surface, 3dkt assembly 1_P SES surface, 3dkt assembly
1_P SES surface, 3dkt assembly 1_P SES surface, 3dkt assembly 1_Q SES surface,
3dkt assembly 1_Q SES surface, 3dkt assembly 1_Q SES surface, 3dkt assembly
1_Q SES surface, 3dkt assembly 1_Q SES surface, 3dkt assembly 1_Q SES surface,
3dkt assembly 1_R SES surface, 3dkt assembly 1_R SES surface, 3dkt assembly
1_R SES surface, 3dkt assembly 1_R SES surface, 3dkt assembly 1_R SES surface,
3dkt assembly 1_R SES surface, 3dkt assembly 1_S SES surface, 3dkt assembly
1_S SES surface, 3dkt assembly 1_S SES surface, 3dkt assembly 1_S SES surface,
3dkt assembly 1_S SES surface, 3dkt assembly 1_S SES surface, 3dkt assembly
1_T SES surface, 3dkt assembly 1_T SES surface, 3dkt assembly 1_T SES surface,
3dkt assembly 1_T SES surface, 3dkt assembly 1_T SES surface, 3dkt assembly
1_T SES surface, 132420 atoms, 3300 bonds  

> transparency (#!2 & sel) 50

> hide sel atoms

> color (#!2 & sel) dark gray

> transparency (#!2 & sel) 50

> lighting soft

> lighting soft

> lighting simple

> lighting simple

> lighting soft

> lighting full

> lighting soft

> lighting shadows true intensity 0.5

> lighting shadows false

> graphics silhouettes false

> lighting full

> lighting soft

> select clear

> select #2.10

2141 atoms, 264 residues, 1 model selected  

> select #2.11

56 atoms, 8 residues, 1 model selected  

> color (#!2 & sel) yellow

> transparency (#!2 & sel) 80

> transparency (#!2 & sel) 0

> surface style #2.11 solid

> surface style #2.11 mesh

> surface style #2.11 dot

> select clear

> select #2.20

56 atoms, 8 residues, 1 model selected  

> select #2.19

56 atoms, 8 residues, 1 model selected  

> select #2.20

56 atoms, 8 residues, 1 model selected  

> select #2.19

56 atoms, 8 residues, 1 model selected  

> select #2.20

56 atoms, 8 residues, 1 model selected  

> select #2.19

56 atoms, 8 residues, 1 model selected  

> select clear

Drag select of 3dkt assembly 1_A SES surface, 240430 of 248730 triangles, 3dkt
assembly 1_A SES surface, 3dkt assembly 1_A SES surface, 3dkt assembly 1_A SES
surface, 193579 of 248730 triangles, 3dkt assembly 1_A SES surface, 3dkt
assembly 1_A SES surface, 248358 of 248730 triangles, 3dkt assembly 1_B SES
surface, 249992 of 250398 triangles, 3dkt assembly 1_B SES surface, 239158 of
250398 triangles, 3dkt assembly 1_B SES surface, 3dkt assembly 1_B SES
surface, 172221 of 250398 triangles, 3dkt assembly 1_B SES surface, 3dkt
assembly 1_B SES surface, 3dkt assembly 1_C SES surface, 240636 of 249210
triangles, 3dkt assembly 1_C SES surface, 3dkt assembly 1_C SES surface, 3dkt
assembly 1_C SES surface, 191783 of 249210 triangles, 3dkt assembly 1_C SES
surface, 3dkt assembly 1_C SES surface, 3dkt assembly 1_D SES surface, 188032
of 248164 triangles, 3dkt assembly 1_D SES surface, 3dkt assembly 1_D SES
surface, 3dkt assembly 1_D SES surface, 212406 of 248164 triangles, 3dkt
assembly 1_D SES surface, 3dkt assembly 1_D SES surface, 3dkt assembly 1_E SES
surface, 188706 of 247814 triangles, 3dkt assembly 1_E SES surface, 3dkt
assembly 1_E SES surface, 3dkt assembly 1_E SES surface, 214087 of 247814
triangles, 3dkt assembly 1_E SES surface, 3dkt assembly 1_E SES surface,
242687 of 247814 triangles, 3dkt assembly 1_F SES surface, 3dkt assembly 1_F
SES surface, 3dkt assembly 1_F SES surface, 3dkt assembly 1_F SES surface,
3dkt assembly 1_F SES surface, 3dkt assembly 1_F SES surface, 3dkt assembly
1_G SES surface, 3dkt assembly 1_G SES surface, 3dkt assembly 1_G SES surface,
3dkt assembly 1_G SES surface, 3dkt assembly 1_G SES surface, 249337 of 250200
triangles, 3dkt assembly 1_G SES surface, 3dkt assembly 1_H SES surface,
247885 of 248868 triangles, 3dkt assembly 1_H SES surface, 3dkt assembly 1_H
SES surface, 243657 of 248868 triangles, 3dkt assembly 1_H SES surface, 3dkt
assembly 1_H SES surface, 3dkt assembly 1_H SES surface, 3dkt assembly 1_I SES
surface, 232557 of 245314 triangles, 3dkt assembly 1_I SES surface, 3dkt
assembly 1_I SES surface, 3dkt assembly 1_I SES surface, 3dkt assembly 1_I SES
surface, 3dkt assembly 1_I SES surface, 3dkt assembly 1_J SES surface, 3dkt
assembly 1_J SES surface, 3dkt assembly 1_J SES surface, 3dkt assembly 1_J SES
surface, 3dkt assembly 1_J SES surface, 3dkt assembly 1_J SES surface, 3dkt
assembly 1_K SES surface, 3dkt assembly 1_K SES surface, 3dkt assembly 1_K SES
surface, 3dkt assembly 1_K SES surface, 3dkt assembly 1_K SES surface, 3dkt
assembly 1_K SES surface, 3dkt assembly 1_L SES surface, 3dkt assembly 1_L SES
surface, 3dkt assembly 1_L SES surface, 3dkt assembly 1_L SES surface, 3dkt
assembly 1_L SES surface, 3dkt assembly 1_L SES surface, 3dkt assembly 1_M SES
surface, 3dkt assembly 1_M SES surface, 3dkt assembly 1_M SES surface, 3dkt
assembly 1_M SES surface, 3dkt assembly 1_M SES surface, 3dkt assembly 1_M SES
surface, 3dkt assembly 1_N SES surface, 3dkt assembly 1_N SES surface, 3dkt
assembly 1_N SES surface, 3dkt assembly 1_N SES surface, 3dkt assembly 1_N SES
surface, 3dkt assembly 1_N SES surface, 3dkt assembly 1_O SES surface, 3dkt
assembly 1_O SES surface, 3dkt assembly 1_O SES surface, 3dkt assembly 1_O SES
surface, 3dkt assembly 1_O SES surface, 3dkt assembly 1_O SES surface, 3dkt
assembly 1_P SES surface, 3dkt assembly 1_P SES surface, 3dkt assembly 1_P SES
surface, 3dkt assembly 1_P SES surface, 3dkt assembly 1_P SES surface, 3dkt
assembly 1_P SES surface, 3dkt assembly 1_Q SES surface, 3dkt assembly 1_Q SES
surface, 3dkt assembly 1_Q SES surface, 3dkt assembly 1_Q SES surface, 3dkt
assembly 1_Q SES surface, 3dkt assembly 1_Q SES surface, 3dkt assembly 1_R SES
surface, 3dkt assembly 1_R SES surface, 3dkt assembly 1_R SES surface, 3dkt
assembly 1_R SES surface, 3dkt assembly 1_R SES surface, 3dkt assembly 1_R SES
surface, 3dkt assembly 1_S SES surface, 3dkt assembly 1_S SES surface, 3dkt
assembly 1_S SES surface, 3dkt assembly 1_S SES surface, 3dkt assembly 1_S SES
surface, 3dkt assembly 1_S SES surface, 3dkt assembly 1_T SES surface, 3dkt
assembly 1_T SES surface, 3dkt assembly 1_T SES surface, 3dkt assembly 1_T SES
surface, 3dkt assembly 1_T SES surface, 3dkt assembly 1_T SES surface  

> select clear

Drag select of 3dkt assembly 1_A SES surface, 3dkt assembly 1_A SES surface,
3dkt assembly 1_A SES surface, 3dkt assembly 1_A SES surface, 3dkt assembly
1_A SES surface, 3dkt assembly 1_A SES surface, 3dkt assembly 1_B SES surface,
3dkt assembly 1_B SES surface, 3dkt assembly 1_B SES surface, 3dkt assembly
1_B SES surface, 3dkt assembly 1_B SES surface, 3dkt assembly 1_B SES surface,
3dkt assembly 1_C SES surface, 3dkt assembly 1_C SES surface, 3dkt assembly
1_C SES surface, 3dkt assembly 1_C SES surface, 3dkt assembly 1_C SES surface,
3dkt assembly 1_C SES surface, 3dkt assembly 1_D SES surface, 3dkt assembly
1_D SES surface, 3dkt assembly 1_D SES surface, 3dkt assembly 1_D SES surface,
3dkt assembly 1_D SES surface, 3dkt assembly 1_D SES surface, 3dkt assembly
1_E SES surface, 3dkt assembly 1_E SES surface, 3dkt assembly 1_E SES surface,
3dkt assembly 1_E SES surface, 3dkt assembly 1_E SES surface, 3dkt assembly
1_E SES surface, 3dkt assembly 1_F SES surface, 3dkt assembly 1_F SES surface,
3dkt assembly 1_F SES surface, 3dkt assembly 1_F SES surface, 3dkt assembly
1_F SES surface, 3dkt assembly 1_F SES surface, 3dkt assembly 1_G SES surface,
3dkt assembly 1_G SES surface, 3dkt assembly 1_G SES surface, 3dkt assembly
1_G SES surface, 3dkt assembly 1_G SES surface, 3dkt assembly 1_G SES surface,
3dkt assembly 1_H SES surface, 3dkt assembly 1_H SES surface, 3dkt assembly
1_H SES surface, 3dkt assembly 1_H SES surface, 3dkt assembly 1_H SES surface,
3dkt assembly 1_H SES surface, 3dkt assembly 1_I SES surface, 3dkt assembly
1_I SES surface, 3dkt assembly 1_I SES surface, 3dkt assembly 1_I SES surface,
3dkt assembly 1_I SES surface, 3dkt assembly 1_I SES surface, 3dkt assembly
1_J SES surface, 3dkt assembly 1_J SES surface, 3dkt assembly 1_J SES surface,
3dkt assembly 1_J SES surface, 3dkt assembly 1_J SES surface, 3dkt assembly
1_J SES surface, 3dkt assembly 1_K SES surface, 3dkt assembly 1_K SES surface,
3dkt assembly 1_K SES surface, 3dkt assembly 1_K SES surface, 3dkt assembly
1_K SES surface, 3dkt assembly 1_K SES surface, 3dkt assembly 1_L SES surface,
3dkt assembly 1_L SES surface, 3dkt assembly 1_L SES surface, 3dkt assembly
1_L SES surface, 3dkt assembly 1_L SES surface, 3dkt assembly 1_L SES surface,
3dkt assembly 1_M SES surface, 3dkt assembly 1_M SES surface, 3dkt assembly
1_M SES surface, 3dkt assembly 1_M SES surface, 3dkt assembly 1_M SES surface,
3dkt assembly 1_M SES surface, 3dkt assembly 1_N SES surface, 3dkt assembly
1_N SES surface, 3dkt assembly 1_N SES surface, 3dkt assembly 1_N SES surface,
3dkt assembly 1_N SES surface, 3dkt assembly 1_N SES surface, 3dkt assembly
1_O SES surface, 3dkt assembly 1_O SES surface, 3dkt assembly 1_O SES surface,
3dkt assembly 1_O SES surface, 3dkt assembly 1_O SES surface, 3dkt assembly
1_O SES surface, 3dkt assembly 1_P SES surface, 3dkt assembly 1_P SES surface,
3dkt assembly 1_P SES surface, 3dkt assembly 1_P SES surface, 3dkt assembly
1_P SES surface, 3dkt assembly 1_P SES surface, 3dkt assembly 1_Q SES surface,
3dkt assembly 1_Q SES surface, 3dkt assembly 1_Q SES surface, 3dkt assembly
1_Q SES surface, 3dkt assembly 1_Q SES surface, 3dkt assembly 1_Q SES surface,
3dkt assembly 1_R SES surface, 3dkt assembly 1_R SES surface, 3dkt assembly
1_R SES surface, 3dkt assembly 1_R SES surface, 3dkt assembly 1_R SES surface,
3dkt assembly 1_R SES surface, 3dkt assembly 1_S SES surface, 3dkt assembly
1_S SES surface, 3dkt assembly 1_S SES surface, 3dkt assembly 1_S SES surface,
3dkt assembly 1_S SES surface, 3dkt assembly 1_S SES surface, 3dkt assembly
1_T SES surface, 3dkt assembly 1_T SES surface, 3dkt assembly 1_T SES surface,
3dkt assembly 1_T SES surface, 3dkt assembly 1_T SES surface, 3dkt assembly
1_T SES surface  

> transparency #2.1-20 20

> transparency #2.1-20 80

> transparency #2.1-20 90

> select clear

> select #2.11

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> surface style #2.11 solid

> select clear

> select #2.11

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 30

> transparency (#!2 & sel) 10

> transparency (#!2 & sel) 0

> select clear

> select #2.12

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select #2.13

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select #2.14

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select #2.15

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select #2.16

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select #2.17

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select #2.18

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select #2.19

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select #2.20

56 atoms, 8 residues, 1 model selected  

> transparency (#!2 & sel) 0

> select clear

> select #2

22070 atoms, 22370 bonds, 2820 residues, 1 model selected  

> transparency (#!2 & sel) 70

> sequence chain #1/K#1/L#1/M#1/N#1/O#1/P#1/Q#1/R#1/S#1/T

Alignment identifier is 1  

> sequence chain #1/A#1/B#1/C#1/D#1/E#1/F#1/G#1/H#1/I#1/J

Alignment identifier is 2  

> sequence chain #1/K#1/L#1/M#1/N#1/O#1/P#1/Q#1/R#1/S#1/T

Alignment identifier is 3  

> transparency #2 0

> select clear

> lighting soft

> close session

> open 3dkt format mmcif fromDatabase pdb

3dkt title:  
Crystal structure of Thermotoga maritima encapsulin [more info...]  
  
Chain information for 3dkt #1  
---  
Chain | Description  
A B C D E F G H I J | Maritimacin  
K L M N O P Q R S T | Putative uncharacterized protein  
  
3dkt mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> sym #1 assembly 1

> view

> show #2 surfaces

> save "C:/Users/nuren/OneDrive - The University of Sydney (Staff)/Cover
> image-ChemSysChem/shell.stl"

> hide #!2 atoms

> hide #!2 cartoons

> save "C:/Users/nuren/OneDrive - The University of Sydney (Staff)/Cover
> image-ChemSysChem/enc.glb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\\__init__.py", line 39, in save  
gltf.write_gltf(session, path, models, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 292, in write_gltf  
preserve_transparency)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 398, in nodes_and_meshes  
geom = [combine_instance_geometry(va, na, vc, ta, pos, ic)]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 555, in combine_instance_geometry  
ivc = single_vertex_color(len(va), instance_colors[i])  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 555, in combine_instance_geometry  
ivc = single_vertex_color(len(va), instance_colors[i])  
  
See log for complete Python traceback.  
  

> save "C:/Users/nuren/OneDrive - The University of Sydney (Staff)/Cover
> image-ChemSysChem/enc.glb"

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-packages\chimerax\ui\gui.py",
line 1574, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 102, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 113, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 48, in display  
run(session, cmd)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
results = command.run(text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2805, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\\__init__.py", line 39, in save  
gltf.write_gltf(session, path, models, **kw)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 292, in write_gltf  
preserve_transparency)  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 398, in nodes_and_meshes  
geom = [combine_instance_geometry(va, na, vc, ta, pos, ic)]  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 555, in combine_instance_geometry  
ivc = single_vertex_color(len(va), instance_colors[i])  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
IndexError: index 1 is out of bounds for axis 0 with size 1  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 555, in combine_instance_geometry  
ivc = single_vertex_color(len(va), instance_colors[i])  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 457.51
OpenGL renderer: GeForce RTX 2060 SUPER/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: System manufacturer
Model: System Product Name
OS: Microsoft Windows 10 Education (Build 19041)
Memory: 17,085,153,280
MaxProcessMemory: 137,438,953,344
CPU: 24 AMD Ryzen 9 3900XT 12-Core Processor           "
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.3
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1

Change History (2)

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Write GLTF: index 1 is out of bounds for axis 0 with size 1

comment:2 by Tom Goddard, 4 years ago

Resolution: → duplicate
Status: assigned → closed

Fixed 5 months ago. Ticket #4788

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