Opened 7 years ago

Closed 7 years ago

#1259 closed defect (fixed)

1tqn assembly: incomplete multiline data value

Reported by: lpravda@… Owned by: Greg Couch
Priority: normal Milestone:
Component: Input/Output Version: 0.7
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Darwin-17.7.0-x86_64-i386-64bit
ChimeraX Version: 0.7 (2018-08-07)
Description
The following file could not be parsed. https://www.ebi.ac.uk/pdbe/coordinates/1tqn/assembly?id=1 Not sure what is wrong with it.

Log:
UCSF ChimeraX version: 0.7 (2018-08-07)  
OpenGL version: 4.1 ATI-1.68.20  
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine  
OpenGL vendor: ATI Technologies Inc.  
How to cite UCSF ChimeraX  

open /Users/lpravda/temp/interactions/tq/1tqn/1tqn.cif

Summary of feedback from opening
/Users/lpravda/temp/interactions/tq/1tqn/1tqn.cif  
---  
notes | No PDBx fixed column width tables  
No PDBx keywords  
  
Traceback (most recent call last):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 517, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 111, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 508, in open  
    session, filenames, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/__init__.py", line 50, in open_file  
    log_info=log_info)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 53, in open_mmcif  
    pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets,
atomic)  
_mmcif.error: incomplete multiline data value near line 135  
  

_mmcif.error: incomplete multiline data value near line 135  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 53, in open_mmcif  
pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic)  
  
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.  

open /Users/lpravda/temp/interactions/tq/1tqn/1tqn.cif

Summary of feedback from opening
/Users/lpravda/temp/interactions/tq/1tqn/1tqn.cif  
---  
notes | No PDBx fixed column width tables  
No PDBx keywords  
  
Traceback (most recent call last):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 517, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 111, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 508, in open  
    session, filenames, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/__init__.py", line 50, in open_file  
    log_info=log_info)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 53, in open_mmcif  
    pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets,
atomic)  
_mmcif.error: incomplete multiline data value near line 135  
  

_mmcif.error: incomplete multiline data value near line 135  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 53, in open_mmcif  
pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic)  
  
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.  

open /Users/lpravda/temp/interactions/tq/1tqn/1tqn.cif

Summary of feedback from opening
/Users/lpravda/temp/interactions/tq/1tqn/1tqn.cif  
---  
notes | No PDBx fixed column width tables  
No PDBx keywords  
  
Traceback (most recent call last):  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/ui/gui.py", line 517, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/run.py", line 31, in run  
    results = command.run(text, log=log)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 111, in open  
    models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/models.py", line 508, in open  
    session, filenames, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/core/io.py", line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/__init__.py", line 50, in open_file  
    log_info=log_info)  
  File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 53, in open_mmcif  
    pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets,
atomic)  
_mmcif.error: incomplete multiline data value near line 135  
  

_mmcif.error: incomplete multiline data value near line 135  
  
File
"/Applications/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-
packages/chimerax/atomic/mmcif/mmcif.py", line 53, in open_mmcif  
pointers = _mmcif.parse_mmCIF_file(path, categories, log, coordsets, atomic)  
  
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: 4.1 ATI-1.68.20
OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (4)

comment:1 by Eric Pettersen, 7 years ago

Cc: Tom Goddard added
Component: Unassigned → Input/Output
Owner: set to Greg Couch
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → 1tqn assembly: incomplete multiline data value
Version: → 0.7

Reported by Lukas Pravda

comment:2 by Greg Couch, 7 years ago

Status: assigned → accepted

Looking into this. I can reproduce it.

comment:3 by Greg Couch, 7 years ago

The bug is that ChimeraX's mmCIF parser is not expecting any whitespace other than <eol> after the semicolon that terminates the multi-line constant.

comment:4 by Greg Couch, 7 years ago

Resolution: → fixed
Status: accepted → closed

The fix is in. Will be in builds dated 2018-8-27 or later.

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