Open pdbdev 10: File is not a zip file

[mr.edvinas.stankunas@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.17134
ChimeraX Version: 0.8 (2018-10-30)
Description
Command: open 10 from pdbdev

Log:
UCSF ChimeraX version: 0.8 (2018-10-30)  
How to cite UCSF ChimeraX  

open 1 fromDatabase pdbdev

open 1 fromDatabase pdbdev

Summary of feedback from opening 1 fetched from pdbdev  
---  
notes | aligned 3f3f A, 308 residues, rms 1.4  
aligned 2pm7 D, 288 residues, rms 1.345  
  
Entities and chains for PDBDEV_00000001.cif  
---  
Entity | Chains  
Nup120 | C  
Nup133 | D  
Nup145c | E  
Nup84 | A  
Nup85 | B  
Sec13 | G  
Seh1 | F  
  
3f3f A title:  
Crystal structure of the nucleoporin pair Nup85-Seh1, space group P21
[more info...]  
  
2pm7 D title:  
Crystal structure of yeast Sec13/31 edge element of the COPII vesicular coat,
selenomethionine version [more info...]  
  
Opened IHM file C:\Users\Edvinas\Downloads\ChimeraX\PDBDev\PDBDEV_00000001.cif  
2 xray and nmr models  
7 sequence alignments  
20 templates  
164 DSS crosslinks, 127 EDC crosslinks  
1 electron microscopy images  
2 sphere models  
14 localization maps  

~select #1

~select #1

select subtract #1

select subtract #1

Nothing selected  

select #1

select #1

13397 atoms, 4834 bonds, 9124 pseudobonds, 82 models selected  

hide selAtoms

hide selAtoms

show selAtoms ribbons

show selAtoms ribbons

hide selAtoms ribbons

hide selAtoms ribbons

show selAtoms ribbons

show selAtoms ribbons

hide selAtoms surfaces

hide selAtoms surfaces

open 10 fromDatabase pdbdev

open 10 fromDatabase pdbdev

Traceback (most recent call last):  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 224, in execute  
    cmd.run(cmd_text)  
  File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2563, 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 356, 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 416, 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 271, in read_starting_models  
    xmodels = self.read_experimental_models()  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 325, in read_experimental_models  
    models = d.models(self.session)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 1308, in models  
    fs = finfo.stream(session)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 1156, in stream  
    f = self._open_doi_file(session, self.file_path, mode, uncompress)  
  File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\ihm\ihm.py",
line 1189, in _open_doi_file  
    f = fetch_doi_archive_file(session, r.ref, r.url, 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.  
  




OpenGL version: 3.3.0 - Build 20.19.15.4531
OpenGL renderer: Intel(R) HD Graphics 5500
OpenGL vendor: Intel

[Tom Goddard]

This error must be because a downloaded zip file in ~/Downloads/ChimeraX/DOI/... is bad -- either the file is truncated or it is corrupted. Unfortunately the error message does not say which zip file has the problem. I've added additional error reporting to list at the top of the log which file is bad.

Try tomorrow's daily build to find which downloaded file is truncated / corrupted. Please tell me which file it is and also the file size as I want to know what happened.

I may put in code that deletes corrupted downloaded files and retries the download. But I've never seen this happen before so I want to understand you ended up with such a file before I make complex code to handle it.

[mr.edvinas.stankunas@…]

Fortunately, I have managed to circumvent the error by reinstalling Chimera X and unticking box “Precompile Python …” in the last step. Thank you for your time allocated. 

Sent from Mail for Windows 10

From: ChimeraX
Sent: Wednesday, October 31, 2018 3:07 AM
Cc: goddard@cgl.ucsf.edu; mr.edvinas.stankunas@gmail.com
Subject: Re: [ChimeraX] #1398: Open pdbdev 10: File is not a zip file

#1398: Open pdbdev 10: File is not a zip file
---------------------------------------------+----------------------
          Reporter:  mr.edvinas.stankunas@…  |      Owner:  goddard
              Type:  defect                  |     Status:  assigned
          Priority:  normal                  |  Milestone:
         Component:  Higher-Order Structure  |    Version:
        Resolution:                          |   Keywords:
        Blocked By:                          |   Blocking:
Notify when closed:                          |   Platform:  all
           Project:  ChimeraX                |
---------------------------------------------+----------------------

Comment (by goddard):

 This error must be because a downloaded zip file in
 ~/Downloads/ChimeraX/DOI/... is bad -- either the file is truncated or it
 is corrupted.  Unfortunately the error message does not say which zip file
 has the problem.  I've added additional error reporting to list at the top
 of the log which file is bad.

 Try tomorrow's daily build to find which downloaded file is truncated /
 corrupted.  Please tell me which file it is and also the file size as I
 want to know what happened.

 I may put in code that deletes corrupted downloaded files and retries the
 download.  But I've never seen this happen before so I want to understand
 you ended up with such a file before I make complex code to handle it.

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/1398#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker



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[Tom Goddard]

I would not expect reinstalling ChimeraX to fix this problem. When I said in my previous comment that a file was corrupted I was referring to a PDBDev zip file, not a ChimeraX file. Byte compiling ChimeraX Python should make no difference -- if you don't do that when you install, it will do that when you first run ChimeraX.

But if it is working now that is good.