id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1856 OpenGL error, glClear: invalid framebuffer operation monica.mittal@… Tristan Croll "{{{ 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. }}} " defect closed normal Graphics can't reproduce Tom Goddard all ChimeraX