Opened 5 years ago

Closed 5 years ago

#3265 closed defect (fixed)

glTF save error

Reported by: thibault.tubiana@… 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:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 1.0rc202005190628 (2020-05-19 06:28:14 UTC)
Description
I loaded a protein (1rlw), added a surface with hydrophobicity coloring and then I tried to export it to GLB format (File > Save > output.glb).

See attachment for the error message.

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 1.0rc202005190628 (2020-05-19)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/thibault/3t5d.cif

No such file/path: /Users/thibault/3t5d.cif  

> open /Users/thibault/Downloads/emd_6422.map

No such file/path: /Users/thibault/Downloads/emd_6422.map  

> hide atoms

> open /Users/thibault/Downloads/emd_1273.map

No such file/path: /Users/thibault/Downloads/emd_1273.map  

> save /Users/thibault/Desktop/image2.png supersample 3

> open /Users/thibault/1rlw.cif

Summary of feedback from opening /Users/thibault/1rlw.cif  
---  
notes | Fetching CCD CD from http://ligand-expo.rcsb.org/reports/C/CD/CD.cif  
Fetching CCD CA from http://ligand-expo.rcsb.org/reports/C/CA/CA.cif  
  
1rlw.cif title:  
Calcium-phospholipid binding domain from cytosolic phospholipase A2 [more
info...]  
  
Chain information for 1rlw.cif #1  
---  
Chain | Description  
A | phospholipase A2  
  
Non-standard residues in 1rlw.cif #1  
---  
CA — calcium ion  
CD — cadmium ion  
  

> mlp

Map values for surface "1rlw.cif_A SES surface": minimum -25.79, mean -5.501,
maximum 21.77  

> hide surfaces

> show surfaces

> color bfactor

1156 atoms, 281 residues, 1 surfaces, atom bfactor range 2.06 to 77.3  

> mlp

Map values for surface "1rlw.cif_A SES surface": minimum -25.79, mean -5.501,
maximum 21.77  
Alignment identifier is 1.A  
Destroying pre-existing alignment with identifier 1.A  
Alignment identifier is 1.A  

> interfaces ~solvent

0 buried areas:  

> lighting simple

> lighting full

> lighting flat

> lighting full

> lighting shadows false

> lighting shadows true

> graphics silhouettes false

> graphics silhouettes true

> save /Users/thibault/test_coloing.glb

Traceback (most recent call last):  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1544, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 106, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 117, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
run(session, cmd)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/gltf/__init__.py", line 39, in save  
gltf.write_gltf(session, path, **kw)  
TypeError: write_gltf() missing 1 required positional argument: 'models'  
  
TypeError: write_gltf() missing 1 required positional argument: 'models'  
  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/gltf/__init__.py", line 39, in save  
gltf.write_gltf(session, path, **kw)  
  
See log for complete Python traceback.  
  

> save /Users/thibault/test.glb

Traceback (most recent call last):  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 1544, in <lambda>  
action.triggered.connect(lambda arg, cb = callback: cb())  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 106, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 117, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
run(session, cmd)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/gltf/__init__.py", line 39, in save  
gltf.write_gltf(session, path, **kw)  
TypeError: write_gltf() missing 1 required positional argument: 'models'  
  
TypeError: write_gltf() missing 1 required positional argument: 'models'  
  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/gltf/__init__.py", line 39, in save  
gltf.write_gltf(session, path, **kw)  
  
See log for complete Python traceback.  
  

> save test.glb

Traceback (most recent call last):  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 258, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 66, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2802, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/save_command/cmd.py", line 79, in provider_save  
mgr).save(session, path, **provider_kw)  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/gltf/__init__.py", line 39, in save  
gltf.write_gltf(session, path, **kw)  
TypeError: write_gltf() missing 1 required positional argument: 'models'  
  
TypeError: write_gltf() missing 1 required positional argument: 'models'  
  
File
"/private/var/folders/kj/ppryv47n1jj612f2zvkgf23w0000gn/T/AppTranslocation/11108151-8606-443C-8FCD-28EDE99B1930/d/ChimeraX-1.0-rc-2020.05.19.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/gltf/__init__.py", line 39, in save  
gltf.write_gltf(session, path, **kw)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.16
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro15,2
      Processor Name: Intel Core i5
      Processor Speed: 2,4 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 256 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      Boot ROM Version: 1037.80.53.0.0 (iBridge: 17.16.13050.0.0,0)

Software:

    System Software Overview:

      System Version: macOS 10.14.6 (18G3020)
      Kernel Version: Darwin 18.7.0
      Time since boot: 11 days 22:08

Graphics/Displays:

    Intel Iris Plus Graphics 655:

      Chipset Model: Intel Iris Plus Graphics 655
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x3ea5
      Revision ID: 0x0001
      Metal: Supported, feature set macOS GPUFamily2 v1
      Displays:
        2369M:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: BCOD49A000007
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DisplayPort
        MSI MAG271C:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60 Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: No
          Connection Type: DVI or HDMI
          Adapter Firmware Version:  3.0c

PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.8
File attachment: error_chimeraX.txt

error_chimeraX.txt​

Attachments (1)

error_chimeraX.txt​ (2.5 KB ) - added by thibault.tubiana@… 5 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (3)

by thibault.tubiana@…, 5 years ago

Attachment: error_chimeraX.txt​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 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 → glTF save error

comment:2 by Eric Pettersen, 5 years ago

Resolution: → fixed
Status: accepted → closed

Hi Thibault,

Thanks for reporting this problem. I have just fixed it now, and the fix will be in the next release candidate.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

Note: See TracTickets for help on using tickets.