OpenGL error, glClear: invalid framebuffer operation

[monica.mittal@…]

The following bug report has been submitted:
Platform:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-04-16)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.9 (2019-04-16)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> toolshed show Shell

> toolshed show Shell

Unknown command: toolshed
install./ChimeraX_Clipper-0.4-cp37-cp37m-macosx_10_9_x86_64.whl  

> toolshed install ./ChimeraX_Clipper-0.4-cp37-cp37m-macosx_10_9_x86_64.whl

Successfully installed ChimeraX-Clipper-0.4  
Installed ChimeraX-Clipper (0.4)  

'clip' is a prefix of an existing command 'clipper'  

> toolshed install
./ChimeraX_ISOLDE-1.0b2.dev1-cp37-cp37m-macosx_10_9_x86_64.whl

Successfully installed ChimeraX-ISOLDE-1.0b2.dev1  
Installed ChimeraX-ISOLDE (1.0b2.dev1)  

'clip' is a prefix of an existing command 'clipper'  

> toolshed show ISOLDE

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #1  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
1.3/A | predicted microcompartment protein  
  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
Traceback (most recent call last):  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/updateloop.py", line 72, in draw_new_frame  
view.draw(check_for_changes = False)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 159, in draw  
self._draw_scene(camera, drawings)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/view.py", line 201, in _draw_scene  
r.draw_background()  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/opengl.py", line 1027, in draw_background  
GL.glClear(flags)  
File "src/errorchecker.pyx", line 53, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1286,  
description = b'invalid framebuffer operation',  
baseOperation = glClear,  
cArguments = (16640,)  
)  
  
Done loading forcefield  

> toolshed show ISOLDE

Done loading forcefield  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #2  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
2.3/A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #3  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
3.3/A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #4  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
4.3/A | predicted microcompartment protein  
  

> toolshed show ISOLDE

before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #5  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
5.3/A | predicted microcompartment protein  
  
Done loading forcefield  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #6  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
6.3/A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #7  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
7.3/A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb #8  
---  
Chain | Description  
A | predicted microcompartment protein  
  
before.pdb title:  
Crystal structure of etub from clostridium kluyveri [more info...]  
  
Chain information for before.pdb  
---  
Chain | Description  
8.3/A | predicted microcompartment protein  
  

> show #1 target m

> sequence chain #1.3/A

Alignment identifier is 1.3.A  

> view #1 clip false

> set bgColor white

> isolde tutorial

> open 6mhz

Summary of feedback from opening 6mhz fetched from pdb  
---  
notes | Fetching compressed mmCIF 6mhz from
http://files.rcsb.org/download/6mhz.cif  
Fetching CCD AOV from http://ligand-expo.rcsb.org/reports/A/AOV/AOV.cif  
  
6mhz title:  
Vanadate trapped Cryo-EM Structure of E.coli LptB2FG Transporter [more
info...]  
  
Chain information for 6mhz #9  
---  
Chain | Description  
A B | Lipopolysaccharide export system ATP-binding protein LptB  
F | Lipopolysaccharide export system permease protein LptF  
G | Lipopolysaccharide export system permease protein LptG  
  
Non-standard residues in 6mhz #9  
---  
AOV — adp orthovanadate  
  
  

> open 9118 fromDatabase emdb

Summary of feedback from opening 9118 fetched from emdb  
---  
note | Fetching compressed map 9118 from
ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-9118/map/emd_9118.map.gz  
  
Traceback (most recent call last):  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/gui.py", line 536, in customEvent  
func(*args, **kw)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 300, in defer  
cxcmd(session, topic)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ui/widgets/htmlview.py", line 419, in cxcmd  
run(session, cmd)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.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/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2631, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 41, in open  
from_database=from_database, ignore_cache=ignore_cache, **kw))  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 88, in open  
filename, format=format, name=name, ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
return f(*args, **kw)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 434, in fetch_from_database  
models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/fetch.py", line 497, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/emdb_fetch.py", line 48, in fetch_emdb  
models, status = io.open_data(session, filename, format = 'ccp4', name =
emdb_id, **kw)  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 433, in open_data  
models, status = open_func(*args, **kw)  
TypeError: cannot unpack non-iterable NoneType object  
  
TypeError: cannot unpack non-iterable NoneType object  
  
File
"/private/var/folders/4v/t8v097js2pgbfddb73np5b_w0000gn/T/AppTranslocation/33975C13-36F1-4102-9B7A-7F82C7DFDE69/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 433, in open_data  
models, status = open_func(*args, **kw)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.4.7
OpenGL renderer: Intel Iris Pro OpenGL Engine
OpenGL vendor: Intel Inc.

[Tom Goddard]

There are two ChimeraX errors here, one an OpenGL error trying to draw the scene apparently when ISOLDE is loading demo data, and the second appears to be trying to open EMDB data. I looked into the second error -- the code for opening an EMDB map in CCP4 format has no code that returns None, yet the error says it returned None. I wonder if ISOLDE somehow overrode the opening of CCP4 maps.

My best guess is that both of these errors are related to ISOLDE. So I am reassigning to Tristan who wrote ISOLDE.

[tic20@…]

I’ve seen this error once before, when opening a map in the same ChimeraX session where I’d just `toolshed install`ed Clipper and ISOLDE. After restarting ChimeraX the problem went away. Clipper does add an “open” command, but it it’s nothing to do with map files (opens MTZ data) and doesn’t return None.

 

[Tristan Croll]

Doing some spring-cleaning, clearing away old tickets. Haven't seen this error occur again, so chances are it's gone for good.