Problem opening pdbdev 10

[mr.edvinas.stankunas@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.7 (2018-08-07)
Description
(Describe the actions that caused this problem to occur here)
Tried to open 10 from pdbdev using command:
open 10 from pdbdev

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.7 (2018-08-07)  
OpenGL version: 3.3.0 - Build 20.19.15.4531  
OpenGL renderer: Intel(R) HD Graphics 5500  
OpenGL vendor: Intel  
How to cite UCSF ChimeraX  

open 10 fromDatabase pdbdev

Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 205, in execute  
    cmd.run(cmd_text)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 81, in open  
    filename, format=format, name=name, ignore_cache=ignore_cache, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\fetch.py", line 433, in fetch_from_database  
    models, status = df.fetch(session, id, format=format,
ignore_cache=ignore_cache, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\fetch.py", line 496, in fetch  
    return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 327, in fetch_cb  
    return fetch_shim(session, identifier, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 325, in fetch_shim  
    return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ihm\\__init__.py", line 37, in fetch_from_database  
    return fetch_ihm(session, identifier, ignore_cache=ignore_cache)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ihm\fetch_ihm.py", line 41, in fetch_ihm  
    models, status = io.open_data(session, filename, format = 'ihm', name =
name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ihm\\__init__.py", line 24, in open_file  
    return ihm.read_ihm(session, path, file_name, load_ensembles = ensembles)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 37, in read_ihm  
    show_atom_crosslinks = show_atom_crosslinks)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 64, in __init__  
    stmodels, seqmodels = self.read_starting_models(load_linked_files)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 270, in read_starting_models  
    xmodels = self.read_experimental_models()  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 324, in read_experimental_models  
    models = d.models(self.session)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 1267, in models  
    fs = finfo.stream(session)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 1167, in stream  
    f = fetch_doi_archive_file(session, r.ref, r.url, self.file_path)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ihm\doi_fetch.py", line 117, in fetch_doi_archive_file  
    zf = ZipFile(zip_path, 'r')  
  File "C:\Program Files\ChimeraX\bin\lib\zipfile.py", line 1108, in __init__  
    self._RealGetContents()  
  File "C:\Program Files\ChimeraX\bin\lib\zipfile.py", line 1175, in
_RealGetContents  
    raise BadZipFile("File is not a zip file")  
zipfile.BadZipFile: File is not a zip file  
  

zipfile.BadZipFile: File is not a zip file  
  
File "C:\Program Files\ChimeraX\bin\lib\zipfile.py", line 1175, in
_RealGetContents  
raise BadZipFile("File is not a zip file")  
  
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 C:/Users/Edvinas/Desktop/PDBDEV_00000010.ihm

Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ui\gui.py",
line 517, in _qt_safe  
    run(session, "open " \+ quote_if_necessary(paths[0]))  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 31, in run  
    results = command.run(text, log=log)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2561, in run  
    result = ci.function(session, **kw_args)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 41, in open  
    from_database=from_database, ignore_cache=ignore_cache, **kw))  
  File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 62, in handle_unknown_kw  
    return f(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\models.py", line 508, in open  
    session, filenames, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 444, in open_multiple_data  
    models, status = open_data(session, fspec, format=format, name=name, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 404, in open_data  
    models, status = open_func(*args, **kw)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ihm\\__init__.py", line 24, in open_file  
    return ihm.read_ihm(session, path, file_name, load_ensembles = ensembles)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 37, in read_ihm  
    show_atom_crosslinks = show_atom_crosslinks)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 64, in __init__  
    stmodels, seqmodels = self.read_starting_models(load_linked_files)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 270, in read_starting_models  
    xmodels = self.read_experimental_models()  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 324, in read_experimental_models  
    models = d.models(self.session)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 1267, in models  
    fs = finfo.stream(session)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 1167, in stream  
    f = fetch_doi_archive_file(session, r.ref, r.url, self.file_path)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\ihm\doi_fetch.py", line 117, in fetch_doi_archive_file  
    zf = ZipFile(zip_path, 'r')  
  File "C:\Program Files\ChimeraX\bin\lib\zipfile.py", line 1108, in __init__  
    self._RealGetContents()  
  File "C:\Program Files\ChimeraX\bin\lib\zipfile.py", line 1175, in
_RealGetContents  
    raise BadZipFile("File is not a zip file")  
zipfile.BadZipFile: File is not a zip file  
  

zipfile.BadZipFile: File is not a zip file  
  
File "C:\Program Files\ChimeraX\bin\lib\zipfile.py", line 1175, in
_RealGetContents  
raise BadZipFile("File is not a zip file")  
  
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: 3.3.0 - Build 20.19.15.4531
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel

[Tom Goddard]

"open 10 from pdbdev" worked correctly on Windows and Mac in the current ChimeraX daily build.

Your error is with an August 7 , 2018 ChimeraX build.

Try the daily build. We continue to develop the PDBDev IHM file reader and I'm guessing it was broken in your August ChimeraX.