Problem opening various PDBDEV files: File is not a zip file

[benoit.palancade@…]

The following bug report has been submitted:
Platform:        Darwin-18.6.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-06)
Description
ChimeraX does not manage to open the PDBDEV files 10, 11 or 12 (nuclear pore complex integrative map). The following error message is displayed:
File "/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/zipfile.py", line 1289, in _RealGetContents raise BadZipFile("File is not a zip file")

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1 fromDatabase pdbdev ignoreCache true

Summary of feedback from opening 1 fetched from pdbdev  
---  
notes | Fetching IHM 00000001 from https://pdb-
dev.wwpdb.org/static/cif/PDBDEV_00000001.cif  
aligned 3f3f A, 308 residues, rms 1.4  
aligned 2pm7 D, 288 residues, rms 1.345  
aligned ScNup84N_7-488_new2.pdb A, 440 residues, rms 1.315  
aligned ScNup84C_506-726_new2.pdb A, 209 residues, rms 1.359  
aligned ScNup85_44-744_new.pdb B, 604 residues, rms 22.16  
aligned ScNup120_1-1037_new.pdb C, 922 residues, rms 14.52  
aligned ScNup133N_56-480_new.pdb D, 373 residues, rms 1.303  
aligned ScNup133C_490_1157_new.pdb D, 658 residues, rms 1.335  
aligned ScNup145C_126-553_new2.pdb E, 416 residues, rms 1.346  
  
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 /Users/astrid/Downloads/ChimeraX/PDBDev/PDBDEV_00000001.cif  
2 xray and nmr models  
7 comparative models  
7 sequence alignments  
20 templates  
164 DSS crosslinks, 127 EDC crosslinks  
1 electron microscopy images  
2 sphere models  
14 localization maps  

> set bgColor white

Alignment identifier is 1.1.1.1.A  
Alignment identifier is 1.1.1.2.A  
Alignment identifier is 1.1.2.1.B  
Alignment identifier is 1.1.3.1.C  
Alignment identifier is 1.1.4.1.D  
Alignment identifier is 1.1.4.2.D  
Alignment identifier is 1.1.5.1.E  
Alignment identifier is 1.1.6.1.A  
Alignment identifier is 1.1.7.1.D  
Destroying pre-existing alignment with identifier 1.1.1.1.A  
Alignment identifier is 1.1.1.1.A  
Destroying pre-existing alignment with identifier 1.1.1.2.A  
Alignment identifier is 1.1.1.2.A  
Destroying pre-existing alignment with identifier 1.1.2.1.B  
Alignment identifier is 1.1.2.1.B  
Destroying pre-existing alignment with identifier 1.1.3.1.C  
Alignment identifier is 1.1.3.1.C  
Destroying pre-existing alignment with identifier 1.1.4.1.D  
Alignment identifier is 1.1.4.1.D  
Destroying pre-existing alignment with identifier 1.1.4.2.D  
Alignment identifier is 1.1.4.2.D  
Destroying pre-existing alignment with identifier 1.1.5.1.E  
Alignment identifier is 1.1.5.1.E  
Destroying pre-existing alignment with identifier 1.1.6.1.A  
Alignment identifier is 1.1.6.1.A  
Destroying pre-existing alignment with identifier 1.1.7.1.D  
Alignment identifier is 1.1.7.1.D  
Destroying pre-existing alignment with identifier 1.1.1.1.A  
Alignment identifier is 1.1.1.1.A  
Destroying pre-existing alignment with identifier 1.1.1.2.A  
Alignment identifier is 1.1.1.2.A  
Destroying pre-existing alignment with identifier 1.1.2.1.B  
Alignment identifier is 1.1.2.1.B  
Destroying pre-existing alignment with identifier 1.1.3.1.C  
Alignment identifier is 1.1.3.1.C  
Destroying pre-existing alignment with identifier 1.1.4.1.D  
Alignment identifier is 1.1.4.1.D  
Destroying pre-existing alignment with identifier 1.1.4.2.D  
Alignment identifier is 1.1.4.2.D  
Destroying pre-existing alignment with identifier 1.1.5.1.E  
Alignment identifier is 1.1.5.1.E  
Destroying pre-existing alignment with identifier 1.1.6.1.A  
Alignment identifier is 1.1.6.1.A  
Destroying pre-existing alignment with identifier 1.1.7.1.D  
Alignment identifier is 1.1.7.1.D  

> hide #!1.1 models

> show #!1.1 models

> open 10 fromDatabase pdbdev ignoreCache true

Summary of feedback from opening 10 fetched from pdbdev  
---  
warning | Could not open zip file
/Users/astrid/Downloads/ChimeraX/DOI/10.5281/zenodo.1194547/npc2018-master.zip  
note | Fetching IHM 00000010 from https://pdb-
dev.wwpdb.org/static/cif/PDBDEV_00000010.cif  
  
Traceback (most recent call last):  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 254, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2632, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 43, in open  
db_models = _fetch_from_database(session, db_id, db_name, db_format, name,
ignore_cache, **kw)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 144, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.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/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.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/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/toolshed/info.py", line 381, in fetch_shim  
return f(session, identifier, database_name=database_name,
format_name=format_name, **kw)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/__init__.py", line 37, in fetch_from_database  
return fetch_ihm(session, identifier, ignore_cache=ignore_cache, **kw)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/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
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.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)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/__init__.py", line 24, in open_file  
return ihm.read_ihm(session, path, file_name, load_ensembles = ensembles)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/ihm.py", line 41, in read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/ihm.py", line 69, in __init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/ihm.py", line 250, in read_starting_models  
xmodels = self.read_experimental_models()  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/ihm.py", line 295, in read_experimental_models  
models = d.models(self.session)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/ihm.py", line 1171, in models  
fs = finfo.stream(session)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/ihm.py", line 1018, in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/ihm.py", line 1051, in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/ihm/doi_fetch.py", line 118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/zipfile.py",
line 1222, in __init__  
self._RealGetContents()  
File
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/zipfile.py",
line 1289, 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
"/private/var/folders/my/6ldd5h6d5_10h1ys94k87zw40000gq/T/AppTranslocation/3DA1302A-6354-4D40-B6B2-359418AE0447/d/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/zipfile.py",
line 1289, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.9.22
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 640
OpenGL vendor: Intel Inc.

[Tom Goddard]

Command "open 10 fromDatabase pdbdev ignoreCache true" works fine for me in the same version of ChimeraX (0.9) and macOS (10.14.5) as you are using. My guess is it was some kind of error downloading the entry zip file. The error message says:

warning | Could not open zip file
/Users/astrid/Downloads/ChimeraX/DOI/10.5281/zenodo.1194547/npc2018-master.zip

After I load pdbdev 10 I see this zip file:

$ ls -l ~/Downloads/ChimeraX/DOI/10.5281/zenodo.1194547/npc2018-master.zip
-rw-r--r-- 1 goddard staff 325137309 Mar 9 14:57 /Users/goddard/Downloads/ChimeraX/DOI/10.5281/zenodo.1194547/npc2018-master.zip

Do you have this zip file and does it have the same size 325 Mbytes as shown here?

[Benoit.PALANCADE@…]

Hello,
This zip file was indeed not the right size (227MBytes). I re-downloaded ChimeraX (0.9) and now it finds the correct zip file and opens the structure properly.
Many thanks!


Le 16 juil. 2019 à 19:59, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> a écrit :

#2224: Problem opening various PDBDEV files: File is not a zip file
-----------------------------------------+----------------------
         Reporter:  benoit.palancade@…  |      Owner:  goddard
             Type:  defect              |     Status:  assigned
         Priority:  normal              |  Milestone:
        Component:  Input/Output        |    Version:
       Resolution:                      |   Keywords:
       Blocked By:                      |   Blocking:
Notify when closed:                      |   Platform:  all
          Project:  ChimeraX            |
-----------------------------------------+----------------------
Changes (by goddard):

* cc: ben@…, brinda.vallat@… (added)


Comment:

Command "open 10 fromDatabase pdbdev ignoreCache true" works fine for me
in the same version of ChimeraX (0.9) and macOS (10.14.5) as you are
using.  My guess is it was some kind of error downloading the entry zip
file.  The error message says:

warning | Could not open zip file
/Users/astrid/Downloads/ChimeraX/DOI/10.5281/zenodo.1194547/npc2018-master.zip

After I load pdbdev 10 I see this zip file:

$ ls -l ~/Downloads/ChimeraX/DOI/10.5281/zenodo.1194547/npc2018-master.zip
-rw-r--r--  1 goddard  staff  325137309 Mar  9 14:57
/Users/goddard/Downloads/ChimeraX/DOI/10.5281/zenodo.1194547/npc2018-master.zip

Do you have this zip file and does it have the same size 325 Mbytes as
shown here?

--
Ticket URL: <https://plato.cgl.ucsf.edu/trac/ChimeraX/ticket/2224#comment:2>
ChimeraX <http://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

Benoit PALANCADE, PhD.
CNRS Investigator
Institut Jacques Monod
UMR 7592 CNRS / Université Paris-Diderot
Batiment Buffon
15 rue Helene Brion
75205 PARIS cedex 13
France
--------------------------------
ph. +33 1 57 27 80 39
fax. +33 1 57 27 80 63
--------------------------------
benoit.palancade@ijm.fr<mailto:benoit.palancade@ijm.fr>
--------------------------------
http://orcid.org/0000-0002-3894-9735
--------------------------------

[goddard@…]

I wonder why fetching the file did not report an error that the full file was not successfully downloaded.  If this happens again I will investigate if errors are generated during an incomplete download.

[Tom Goddard]

Truncated zip file fetched. Not sure why that did not generate an error when fetching.