Opened 3 years ago

Closed 3 years ago

Last modified 3 years ago

#6841 closed defect (can't reproduce)

write_gltf: No such file or directory

Reported by: jc3534@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: Tom Goddard
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 1Ik8

Summary of feedback from opening 1Ik8 fetched from pdb  
---  
note | Fetching compressed mmCIF 1ik8 from
http://files.rcsb.org/download/1ik8.cif  
  
1ik8 title:  
NMR structure of Alpha-Bungarotoxin [more info...]  
  
Chain information for 1ik8 #1  
---  
Chain | Description  
A | long neurotoxin 1  
  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset cartoons/nucleotides cylinders/stubs

Changed 0 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> preset "initial styles" sticks

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset cartoons/nucleotides ribbons/slabs

Changed 551 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    nucleotides tube/slab shape box

  

> preset "initial styles" "space-filling (single color)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> preset "initial styles" "original look"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> close session

> open 2abx

Summary of feedback from opening 2abx fetched from pdb  
---  
note | Fetching compressed mmCIF 2abx from
http://files.rcsb.org/download/2abx.cif  
  
2abx title:  
The crystal structure of α-bungarotoxin At 2.5 angstroms resolution. Relation
to solution structure and binding to acetylcholine receptor [more info...]  
  
Chain information for 2abx #1  
---  
Chain | Description  
A B | α-bungarotoxin  
  

> close session

> open 6uwz

Summary of feedback from opening 6uwz fetched from pdb  
---  
notes | Fetching compressed mmCIF 6uwz from
http://files.rcsb.org/download/6uwz.cif  
Fetching CCD MAN from http://ligand-expo.rcsb.org/reports/M/MAN/MAN.cif  
Fetching CCD POV from http://ligand-expo.rcsb.org/reports/P/POV/POV.cif  
Fetching CCD OCT from http://ligand-expo.rcsb.org/reports/O/OCT/OCT.cif  
Fetching CCD P1L from http://ligand-expo.rcsb.org/reports/P/P1L/P1L.cif  
  
6uwz title:  
Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-
bungarotoxin [more info...]  
  
Chain information for 6uwz #1  
---  
Chain | Description  
A D | Acetylcholine receptor subunit α  
B | Acetylcholine receptor subunit δ  
C | Acetylcholine receptor subunit β  
E | Acetylcholine receptor subunit γ  
F G | Alpha-bungarotoxin  
  
Non-standard residues in 6uwz #1  
---  
BMA — beta-D-mannopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
OCT — N-octane  
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)  
  

> select /F:1-73

546 atoms, 565 bonds, 73 residues, 1 model selected  

> preset cartoons/nucleotides cylinders/stubs

Changed 17593 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh tube rad 2 sides 24 thick 0.6
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides stubs

  

> style sel sphere

Changed 546 atom styles  

> preset "initial styles" "space-filling (chain colors)"

Preset implemented in Python; no expansion to individual ChimeraX commands
available.  

> show sel surfaces

> hide sel cartoons

> hide sel atoms

> select

18322 atoms, 18698 bonds, 5 pseudobonds, 2356 residues, 2 models selected  

> hide sel cartoons

> hide sel atoms

> show sel surfaces

> save 6uwz.glb

> save "G:/My Drive/3D protein models/6uwz.gif" width 1340 height 785
> supersample 3

> save 6uwz.glb

> save G:/My Drive/3D protein models/6uwz.glb

Cannot determine format for 'G:/My'  

> CD G:/My Drive/3D protein models

Unknown command: CD G:/My Drive/3D protein models  

> CD G:

Unknown command: CD G:  

> CD G:\My Drive\3D protein models

Unknown command: CD G:\My Drive\3D protein models  

> cd G:\My Drive\3D protein models

Expected a keyword  

> cd G:\My Drive\3D protein models

Expected a keyword  

> cd G:

Current working directory is: G:\  

Unknown or unsupported skia image format  

> save 6uwz.glb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute  
cmd.run(cmd_text)  
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 336, in write_gltf  
file = open(filename, 'wb')  
FileNotFoundError: [Errno 2] No such file or directory: '6uwz.glb'  
  
FileNotFoundError: [Errno 2] No such file or directory: '6uwz.glb'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 336, in write_gltf  
file = open(filename, 'wb')  
  
See log for complete Python traceback.  
  

> save 6uwz.glb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute  
cmd.run(cmd_text)  
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 336, in write_gltf  
file = open(filename, 'wb')  
FileNotFoundError: [Errno 2] No such file or directory: '6uwz.glb'  
  
FileNotFoundError: [Errno 2] No such file or directory: '6uwz.glb'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 336, in write_gltf  
file = open(filename, 'wb')  
  
See log for complete Python traceback.  
  

> open 6uwz

6uwz title:  
Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-
bungarotoxin [more info...]  
  
Chain information for 6uwz #2  
---  
Chain | Description  
A D | Acetylcholine receptor subunit α  
B | Acetylcholine receptor subunit δ  
C | Acetylcholine receptor subunit β  
E | Acetylcholine receptor subunit γ  
F G | Alpha-bungarotoxin  
  
Non-standard residues in 6uwz #2  
---  
BMA — beta-D-mannopyranose  
MAN — alpha-D-mannopyranose  
NAG — 2-acetamido-2-deoxy-beta-D-glucopyranose  
OCT — N-octane  
POV — (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl
2-(trimethylammonio)ethyl phosphate (POPC)  
  

> hide sel cartoons

> hide sel atoms

> show sel surfaces

> preset cartoons/nucleotides licorice/ovals

Changed 35186 atom styles  
Preset expands to these ChimeraX commands:

    
    
    show nucleic
    hide protein|solvent|H
    surf hide
    style (protein|nucleic|solvent) & @@draw_mode=0 stick
    cartoon
    cartoon style modeh def arrows t arrowshelix f arrowscale 2 wid 2 thick 0.4 sides 12 div 20
    cartoon style ~(nucleic|strand) x round
    cartoon style (nucleic|strand) x rect
    cartoon style protein modeh default arrows f x round width 1 thick 1
    cartoon style nucleic x round width 1.6 thick 1.6
    nucleotides tube/slab shape ellipsoid

  

> hide sel cartoons

> show sel surfaces

> hide #!1 models

> ~select #1

7 models selected  

> select

36644 atoms, 37396 bonds, 10 pseudobonds, 4712 residues, 4 models selected  

> show sel & #!2 surfaces

> close session

> open C:\ProgramData\ChimeraX\6uwz.glb format gltf

Opened glTF file containing 1 scenes, 8 nodes, 7 meshes  

> save "G:/My Drive/3D protein models/6uwz.glb"

> close session

> open 1Iob

Summary of feedback from opening 1Iob fetched from pdb  
---  
note | Fetching compressed mmCIF 1iob from
http://files.rcsb.org/download/1iob.cif  
  
1iob title:  
Interleukin-1 β from joint X-ray and NMR refinement [more info...]  
  
Chain information for 1iob #1  
---  
Chain | Description  
A | interleukin-1 β  
  

> close session

> open 5Iob

Summary of feedback from opening 5Iob fetched from pdb  
---  
notes | Fetching compressed mmCIF 5iob from
http://files.rcsb.org/download/5iob.cif  
Fetching CCD GOL from http://ligand-expo.rcsb.org/reports/G/GOL/GOL.cif  
Fetching CCD MES from http://ligand-expo.rcsb.org/reports/M/MES/MES.cif  
  
5iob title:  
Crystal structure of beta-N-acetylglucosaminidase-like protein from
Corynebacterium glutamicum [more info...]  
  
Chain information for 5iob #1  
---  
Chain | Description  
A B C D E F G H | Beta-glucosidase-related glycosidases  
  
Non-standard residues in 5iob #1  
---  
CL — chloride ion  
GOL — glycerol (glycerin; propane-1,2,3-triol)  
MES — 2-(N-morpholino)-ethanesulfonic acid  
SO4 — sulfate ion  
  
5iob mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> close session

> open 5Iov

Summary of feedback from opening 5Iov fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "GLY" near line 18593  
notes | Fetching compressed mmCIF 5iov from
http://files.rcsb.org/download/5iov.cif  
Fetching CCD QEM from http://ligand-expo.rcsb.org/reports/Q/QEM/QEM.cif  
  
5iov title:  
Cryo-EM structure of GluN1/GluN2B NMDA receptor in the
glutamate/glycine/Ro25-6981-bound conformation [more info...]  
  
Chain information for 5iov #1  
---  
Chain | Description  
A C | N-methyl-D-aspartate receptor subunit NR1-8a  
B D | Ionotropic glutamate receptor subunit NR2B  
  
Non-standard residues in 5iov #1  
---  
QEM — 4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol  
  

> show surfaces

> hide cartoons

> hide atoms

> ui mousemode right rotate

> ui mousemode right select

> ui mousemode right translate

> ui mousemode right rotate

> save 5Iov.glb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute  
cmd.run(cmd_text)  
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 336, in write_gltf  
file = open(filename, 'wb')  
FileNotFoundError: [Errno 2] No such file or directory: '5Iov.glb'  
  
FileNotFoundError: [Errno 2] No such file or directory: '5Iov.glb'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 336, in write_gltf  
file = open(filename, 'wb')  
  
See log for complete Python traceback.  
  

> save "G:/My Drive/3D protein models/5Iov.glb"

> save 5Iov.glb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 275, in execute  
cmd.run(cmd_text)  
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 336, in write_gltf  
file = open(filename, 'wb')  
FileNotFoundError: [Errno 2] No such file or directory: '5Iov.glb'  
  
FileNotFoundError: [Errno 2] No such file or directory: '5Iov.glb'  
  
File "C:\Program Files\ChimeraX 1.1\bin\lib\site-
packages\chimerax\gltf\gltf.py", line 336, in write_gltf  
file = open(filename, 'wb')  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 419.17
OpenGL renderer: GeForce MX130/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Manufacturer: Dell Inc.
Model: Latitude 5590
OS: Microsoft Windows 10 Enterprise (Build 19044)
Memory: 17,052,229,632
MaxProcessMemory: 137,438,953,344
CPU: 8 Intel(R) Core(TM) i5-8350U CPU @ 1.70GHz"
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 (4)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → Input/Output
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → write_gltf: No such file or directory

comment:2 by Eric Pettersen, 3 years ago

Hi Jenny,

As per the last commands in your log:

save "G:/My Drive/3D protein models/5Iov.glb"

worked, and:

save 5Iov.glb

failed. The last "cd" command you used that did anything was "cd G:" which resulted in the current folder being G:\. Apparently that folder cannot be written to, causing the save failures you were getting. If you are trying to use 'cd' to change to a directory with a space in it, you need to surround the name with quotes. Alternatively, you can use the name "browse" to bring up a file browser to specify the folder (you can actually do this in any command that take a file or folder name argument). I would strongly recommend upgrading to our latest release (the 1.4 release candidate) because it has many bug fixes relative to the 1.1 release you are using, and in particular the GLTF code has many improvements. Also, reporting bugs against the current release makes it much easier for us to debug them because they will be easier to reproduce.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

comment:3 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: accepted → closed

comment:4 by Tom Goddard, 3 years ago

The error

file = open(filename, 'wb')  
FileNotFoundError: [Errno 2] No such file or directory: '5Iov.glb'

means that the current directory that ChimeraX was in has been deleted, so there is no current directory. If the current directory existed but was not writable the error would have been PermissionError. ChimeraX usually starts in your Desktop directory. Microsoft OneDrive moves your Desktop directory. Possibly you started ChimeraX when using your local Desktop directory and then connected to Microsoft OneDrive which made your local Desktop directory disappear since it provides a cloud based Desktop directory.

ChimeraX does not know how to handle Microsoft OneDrive switching your Desktop directory.

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