Save GLTF: list index out of range

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Linux-5.4.0-135-generic-x86_64-with-debian-bullseye-sid
ChimeraX Version: 0.8 (2018-08-09)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | Error preloading available bundles:  
AttributeError: 'list' object has no attribute 'split'  
  
File "/usr/local/xtal/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 292, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
  
_See log for complete Python traceback._  
  
If you wish to report this error, send mail to [chimerax-  
bugs@cgl.ucsf.edu](mailto:chimerax-bugs@cgl.ucsf.edu) and describe what you  
were doing and include a copy of the contents of the log. Don't include any  
data you wish to remain private since a publicly viewable bug report will be  
created.  
note | Traceback (most recent call last):  
File "/usr/local/xtal/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 337, in __init__  
self.init_available_from_cache(logger)  
File "/usr/local/xtal/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/__init__.py", line 444, in  
init_available_from_cache  
abc.load_from_cache()  
File "/usr/local/xtal/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 61, in load_from_cache  
b = _build_bundle(d)  
File "/usr/local/xtal/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/available.py", line 242, in _build_bundle  
keywords = _extract_extra_keywords(keywords)  
File "/usr/local/xtal/chimerax/lib/python3.6/site-  
packages/chimerax/core/toolshed/installed.py", line 292, in  
_extract_extra_keywords  
all_kwds = [k.strip() for k in kwds.split(',')]  
AttributeError: 'list' object has no attribute 'split'  
  
UCSF ChimeraX version: 0.8 (2018-08-09)  
OpenGL version: 3.3.0 NVIDIA 470.161.03  
OpenGL renderer: NVIDIA GeForce GTX 1080/PCIe/SSE2  
OpenGL vendor: NVIDIA Corporation  
How to cite UCSF ChimeraX  

open /home/wai/HsArgI/4.print3D/M4.pdb

Opened PDB data containing 10627 atoms and 10869 bonds  
Chain information for M4.pdb #1  
---  
Chain | Description  
A | No description available  
B | No description available  
C | No description available  
D | No description available  
  

open /home/wai/HsArgI/4.print3D/M4_HAI+HSA.pdb

Opened PDB data containing 7650 atoms and 7802 bonds  
Chain information for M4_HAI+HSA.pdb #2  
---  
Chain | Description  
C | No description available  
D | No description available  
  
Summary of feedback from opening files  
---  
warning | Ignored bad PDB record found on line 1  
REMARK Fusion protein H6-ABD-linker-HsArgI  
  
Opened PDB data containing 2977 atoms and 3067 bonds  
Opened PDB data containing 4652 atoms and 4742 bonds  
Opened PDB data containing 2998 atoms and 3060 bonds  
Chain information for M4_FcRn.pdb #3.1  
---  
Chain | Description  
A | No description available  
B | No description available  
  
Chain information for M4_HSA.pdb #3.2  
---  
Chain | Description  
C | No description available  
  
Chain information for M4_HAI.pdb #3.3  
---  
Chain | Description  
D | No description available  
  

color selAtoms bychain

color selAtoms bychain

show selAtoms surfaces

hide selAtoms ribbons

save all.obj

save all.glb

Traceback (most recent call last):  
  File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/cmd_line/tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/core/commands/save.py", line 61, in save  
    fmt.export(session, filename, fmt.nicknames[0], **kw)  
  File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/core/io.py", line 198, in export  
    result = self.export_func(session, path, **kw)  
  File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/gltf/__init__.py", line 40, in save_file  
    float_colors=float_colors, transparency=transparency)  
  File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/gltf/gltf.py", line 281, in write_gltf  
    nodes, meshes = nodes_and_meshes(drawings, b, short_vertex_indices,
float_colors, transparency)  
  File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/gltf/gltf.py", line 388, in nodes_and_meshes  
    p0 = pos[0]  
  File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 511, in __getitem__  
    return self.place_list()[i]  
IndexError: list index out of range  
  

IndexError: list index out of range  
  
File "/usr/local/xtal/chimerax/lib/python3.6/site-
packages/chimerax/core/geometry/place.py", line 511, in __getitem__  
return self.place_list()[i]  
  
See log for complete Python traceback.  
  
If you wish to report this error, send mail to chimerax-bugs@cgl.ucsf.edu and
describe what you were doing and include a copy of the contents of the log.
Don't include any data you wish to remain private since a publicly viewable
bug report will be created.  




OpenGL version: 3.3.0 NVIDIA 470.161.03
OpenGL renderer: NVIDIA GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Eric Pettersen]

version 0.8!

[Tom Goddard]

Wow ChimeraX 0.8. The gltf writing code has totally changed so not going to try to find this error. It is looking at positions of a model and the array has zero length which usually indicates that the model was closed. So this is probably a dead model somehow not being cleaned up, possibly because of an earlier error.