Opened 5 years ago

Last modified 5 years ago

#4229 assigned enhancement

IHM: cached zip file corrupted

Reported by: 1449177995@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Input/Output Version:
Keywords: Cc: ben@…
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.18362
ChimeraX Version: 1.1 (2020-09-09 22:22:27 UTC)
Description
(Describe the actions that caused this problem to occur here)I first tried to open with code "open pdbdev:10".And chimeraX signed"no response".So I forced it stop.The next time I tried to open with"pdbdev:10" and it warned "BadZipFile" error. 

And the".cif" files I downloaded from PDB-DEV cannot be seen in with the model. It says no atoms are there.The file is attached with this report.

I don't know how can I fix these.Thank you for you help.

Log:
Startup Messages  
---  
warning | Your computer has Intel graphics driver 7639 with a known bug that
causes all Qt user interface panels to be blank. ChimeraX can partially fix
this but may make some panel titlebars and edges black. Hopefully newer Intel
graphics drivers will fix this.  
  
UCSF ChimeraX version: 1.1 (2020-09-09)  
© 2016-2020 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open C:\Users\14491/Desktop/PDBDEV_00000011.cif

> open C:\Users\14491\Desktop\PDBDEV_00000011.cif format mmcif

> open C:\Users\14491\Desktop\PDBDEV_00000011.cif format mmcif

> open C:\Users\14491\Desktop\PDBDEV_00000011.cif format mmcif

> open C:\Users\14491\Desktop\PDBDEV_00000011.cif format mmcif

> open C:\Users\14491\Desktop\PDBDEV_00000011.cif format mmcif

> set bgColor white

> set bgColor black

> lighting simple

> lighting soft

> set bgColor white

> open C:\Users\14491/Desktop/PDBDEV_00000011.mmcif

No such file/path: C:\Users\14491/Desktop/PDBDEV_00000011.mmcif  

> open C:\Users\14491/Desktop/PDBDEV_00000010.mmcif

> open C:\Users\14491\Desktop\PDBDEV_00000010.mmcif format mmcif

> set bgColor white

> set bgColor black

> open C:\Users\14491\Desktop\PDBDEV_00000010.mmcif format mmcif

> open C:\Users\14491/Desktop/PDBDEV_00000010.cif light simple

'light' has no suffix  

> open C:\Users\14491/Desktop/PDBDEV_00000010.cif lighting simple

'lighting' has no suffix  

> open C:\Users\14491/Desktop/PDBDEV_00000010.cif

> style stick

Changed 0 atom styles  

> style sphere

Changed 0 atom styles  

> style ball

Changed 0 atom styles  

> open C:\Users\14491\Desktop\PDBDEV_00000010.cif format mmcif

> open 2vdw

Summary of feedback from opening 2vdw fetched from pdb  
---  
warning | Unable to infer polymer connectivity due to unspecified label_seq_id
for residue "SAH" near line 20490  
notes | Fetching compressed mmCIF 2vdw from
http://files.rcsb.org/download/2vdw.cif  
Fetching CCD SAH from http://ligand-expo.rcsb.org/reports/S/SAH/SAH.cif  
  
2vdw title:  
Guanosine N7 methyl-transferase sub-complex (D1-D12) of the vaccinia virus
mRNA capping enzyme [more info...]  
  
Chain information for 2vdw #1  
---  
Chain | Description  
A C E G | vaccinia virus capping enzyme D1 subunit  
B D F H | MRNA-capping enzyme small subunit  
  
Non-standard residues in 2vdw #1  
---  
SO4 — sulfate ion  
  
2vdw mmCIF Assemblies  
---  
1| software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> surface #!

Expected an atoms specifier or a keyword  

> surface #1

> surface #2

No atoms specified by #2  

> surface #0

No atoms specified by #0  

> open pdbdev:1

Summary of feedback from opening 1 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1218053\nup84-v1.0.3.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 256, in
read_starting_models  
cmodels = self.read_comparative_models() if load_linked_files else []  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 348, in
read_comparative_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:2

Summary of feedback from opening 2 fetched from pdbdev  
---  
notes | Best scoring model Missing residues for 47 of 216 DSS crosslinks:
/N:16,/N:29,/N:39,/N:44,/N:51...  
Best scoring model Missing residues for 47 of 216 DSS crosslinks:
/N:16,/N:29,/N:39,/N:44,/N:51...  
Best scoring model Missing residues for 71 of 216 DSS crosslinks:
/K:8,/K:16,/K:22,/K:46,/K:81...  
Best scoring model Missing residues for 71 of 216 DSS crosslinks:
/K:8,/K:16,/K:22,/K:46,/K:81...  
aligned 4ifd J, 948 residues, rms 1.331  
aligned 4ifd A, 300 residues, rms 1.265  
aligned 4ifd H, 295 residues, rms 1.281  
aligned 4ifd I, 230 residues, rms 1.271  
aligned 4ifd F, 213 residues, rms 1.274  
aligned 4ifd G, 236 residues, rms 1.264  
aligned 4ifd E, 265 residues, rms 1.208  
aligned 4ifd B, 242 residues, rms 1.313  
aligned 4ifd D, 261 residues, rms 21.74  
aligned 1gfl A, 372 residues, rms 34.29  
aligned 4ifd C, 338 residues, rms 1.279  
aligned 2hbj A, 587 residues, rms 58.74  
aligned 4ifd K, 83 residues, rms 10.51  
could not align aligned Ski7_3izq_modeller_vmd.pdb X to spheres, 0 matching
residues  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 136, in
__init__  
self.localization_models = lmaps = self.read_localization_maps()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 878, in
read_localization_maps  
lmaps = self.read_ensemble_localization_maps()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 898, in
read_ensemble_localization_maps  
map_path = finfo.path(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1137,
in path  
dir = unzip_archive(session, r.ref, r.url)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
138, in unzip_archive  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:3

Summary of feedback from opening 3 fetched from pdbdev  
---  
warning | Ignored bad PDB record found on line 2954  
notes | Fetching IHM 00000003 from https://pdb-
dev.wwpdb.org/cif/PDBDEV_00000003.cif  
Fetching compressed mmCIF 4gwp from http://files.rcsb.org/download/4gwp.cif  
Fetching zip 10.5281/zenodo.802915 mediator-v1.0.3.zip from
https://zenodo.org/record/802915/files/mediator-v1.0.3.zip  
aligned 4gwp G, 170 residues, rms 0.6231  
aligned 4gwp C, 184 residues, rms 0.7367  
aligned 4gwp A, 112 residues, rms 0.5532  
aligned 4gwp B, 492 residues, rms 0.613  
aligned 4gwp E, 253 residues, rms 1.293  
aligned 4gwp F, 209 residues, rms 1.249  
aligned 4gwp D, 121 residues, rms 0.5711  
aligned med7n_med31.pdb A, 73 residues, rms 1.328  
aligned med7c_med21.pdb A, 95 residues, rms 1.367  
aligned med7n_med31.pdb B, 92 residues, rms 1.356  
aligned med7c_med21.pdb B, 127 residues, rms 1.269  
aligned med4_med9.pdb D, 91 residues, rms 1.341  
aligned med4_med9.pdb I, 85 residues, rms 1.421  
aligned med16.NTD.phyre.model.pdb A, 361 residues, rms 1.363  
Fetching zip 10.5281/zenodo.802915 cluster0.zip from
https://zenodo.org/record/802915/files/cluster0.zip  
Fetching zip 10.5281/zenodo.802915 cluster1.zip from
https://zenodo.org/record/802915/files/cluster1.zip  
Fetching zip 10.5281/zenodo.802915 cluster2.zip from
https://zenodo.org/record/802915/files/cluster2.zip  
Fetching zip 10.5281/zenodo.802915 cluster3.zip from
https://zenodo.org/record/802915/files/cluster3.zip  
  
Entities and chains for PDBDEV_00000003.cif  
---  
Entity | Chains  
med1 | N  
med10 | M  
med11 | C  
med14 | O  
med15 | T  
med16 | U  
med17 | D  
med18 | E  
med19 | P  
med2 | Q  
med20 | F  
med21 | L  
med22 | G  
med3 | R  
med31 | K  
med4 | H  
med5 | S  
med6 | A  
med7 | I  
med8 | B  
med9 | J  
  
4gwp G title:  
Structure of the Mediator Head Module from S. cerevisiae [more info...]  
  
4gwp C title:  
Structure of the Mediator Head Module from S. cerevisiae [more info...]  
  
4gwp A title:  
Structure of the Mediator Head Module from S. cerevisiae [more info...]  
  
4gwp B title:  
Structure of the Mediator Head Module from S. cerevisiae [more info...]  
  
4gwp E title:  
Structure of the Mediator Head Module from S. cerevisiae [more info...]  
  
4gwp F title:  
Structure of the Mediator Head Module from S. cerevisiae [more info...]  
  
4gwp D title:  
Structure of the Mediator Head Module from S. cerevisiae [more info...]  
  
med4_med9.pdb D title:  
MED4 AND MED9 STRUCTURE TAKEN FROM LARIVIERE ET AL, NUCLEIC ACIDS RESEARCH.
2013;41:9266-9273. DOI: 10.1093/nar/gkt704. THE MED10 STRUCTURE ALSO PROPOSED
IN THAT WORK IS NOT USED IN THIS STUDY. [more info...]  
  
med7n_med31.pdb A title:  
MED7N and MED31 structures from PDB entry 3FBI, rotated and translated to
align with the MED4-MED9 model [more info...]  
  
med7c_med21.pdb A title:  
MED7C and MED21 structures from PDB entry 1YKH, rotated and translated to
align with the MED4-MED9 model [more info...]  
  
med4_med9.pdb I title:  
MED4 AND MED9 STRUCTURE TAKEN FROM LARIVIERE ET AL, NUCLEIC ACIDS RESEARCH.
2013;41:9266-9273. DOI: 10.1093/nar/gkt704. THE MED10 STRUCTURE ALSO PROPOSED
IN THAT WORK IS NOT USED IN THIS STUDY. [more info...]  
  
med7n_med31.pdb B title:  
MED7N and MED31 structures from PDB entry 3FBI, rotated and translated to
align with the MED4-MED9 model [more info...]  
  
med7c_med21.pdb B title:  
MED7C and MED21 structures from PDB entry 1YKH, rotated and translated to
align with the MED4-MED9 model [more info...]  
  
Opened IHM file C:\Users\14491\Downloads\ChimeraX\PDBDev\PDBDEV_00000003.cif  
11 xray and nmr models  
3 comparative models  
359 DSS crosslinks  
2 electron microscopy images  
4 sphere models  
100 localization maps  

> close #1

> hide #!2.2 models

> show #!2.2 models

> hide #!2.2 models

> hide #!2.1 models

> show #!2.1 models

> hide #!2.1 models

> hide #!2.3 models

> show #!2.3 models

> show #!2.3.2 models

> hide #!2.3.2 models

> hide #!2.3.1 models

> show #!2.3.1 models

> hide #!2.2.3 models

> hide #!2.2.2 models

> hide #2.2.1 models

> hide #!2.1.1 models

> show #!2.1.1 models

> close #2

> open pdbdev:10

Summary of feedback from opening 10 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:10

Summary of feedback from opening 10 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:10

Summary of feedback from opening 10 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:10

Summary of feedback from opening 10 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:10

Summary of feedback from opening 10 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:10

Summary of feedback from opening 10 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  

> open pdbdev:10

Summary of feedback from opening 10 fetched from pdbdev  
---  
warning | Could not open zip file
C:\Users\14491\Downloads\ChimeraX\DOI\10.5281/zenodo.1194547\npc2018-master.zip  
  
Traceback (most recent call last):  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\cmd_line\tool.py", line
275, in execute  
cmd.run(cmd_text)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 100, in cmd_open  
return Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\core\commands\cli.py",
line 2805, in run  
result = ci.function(session, **kw_args)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 128, in provider_open  
(session, ident, format_name, ignore_cache), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 389, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
36, in fetch  
return fetch_ihm(session, ident, ignore_cache, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\fetch_ihm.py", line
41, in fetch_ihm  
name = name, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\manager.py",
line 175, in open_data  
_add_models=False, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 154, in provider_open  
name or model_name_from_path(fi.file_name)), provider_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\open_command\cmd.py",
line 390, in collated_open  
return func(*func_args, **func_kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\\__init__.py", line
25, in open  
return ihm.read_ihm(session, data, file_name, load_ensembles=ensembles, **kw)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 41, in
read_ihm  
show_atom_crosslinks = show_atom_crosslinks)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 71, in
__init__  
stmodels, seqmodels = self.read_starting_models(load_linked_files)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 253, in
read_starting_models  
xmodels = self.read_experimental_models()  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 298, in
read_experimental_models  
models = d.models(self.session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1198,
in models  
fs = finfo.stream(session)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1045,
in stream  
f = self._open_doi_file(session, self.file_path, mode, uncompress)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\ihm.py", line 1078,
in _open_doi_file  
f = fetch_doi_archive_file(session, r.ref, r.url, file_path)  
File "E:\ChimeraX 1.1\bin\lib\site-packages\chimerax\ihm\doi_fetch.py", line
118, in fetch_doi_archive_file  
zf = ZipFile(zip_path, 'r')  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1258, in __init__  
self._RealGetContents()  
File "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, 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 "E:\ChimeraX 1.1\bin\lib\zipfile.py", line 1325, in _RealGetContents  
raise BadZipFile("File is not a zip file")  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 26.20.100.7639
OpenGL renderer: Intel(R) HD Graphics 620
OpenGL vendor: Intel
Manufacturer: Microsoft Corporation
Model: Surface Pro
OS: Microsoft Windows 10 家庭版 (Build 18363)
Memory: 8,507,518,976
MaxProcessMemory: 137,438,953,344
CPU: 4 Intel(R) Core(TM) i5-7300U CPU @ 2.60GHz"
PyQt version: 5.12.3
Compiled Qt version: 5.12.4
Runtime Qt version: 5.12.9
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    Babel: 2.8.0
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2020.6.20
    chardet: 3.0.4
    ChimeraX-AddH: 2.1.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.1
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.6.1
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 1.0.1
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.0
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.0
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.1
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.0
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-CommandLine: 1.1.3
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.1
    ChimeraX-CoreFormats: 1.0
    ChimeraX-coulombic: 1.0.1
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-DataFormats: 1.0
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.0
    ChimeraX-Hbonds: 2.0
    ChimeraX-Help: 1.0
    ChimeraX-HKCage: 1.0
    ChimeraX-IHM: 1.0
    ChimeraX-ImageFormats: 1.0
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0
    ChimeraX-Label: 1.0
    ChimeraX-ListInfo: 1.0
    ChimeraX-Log: 1.1.1
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Map: 1.0.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.0
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 1.1
    ChimeraX-MDcrds: 2.0
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.0
    ChimeraX-mmCIF: 2.2
    ChimeraX-MMTF: 2.0
    ChimeraX-Modeller: 1.0
    ChimeraX-ModelPanel: 1.0
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.0
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0
    ChimeraX-OpenCommand: 1.2.1
    ChimeraX-PDB: 2.1
    ChimeraX-PDBBio: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0
    ChimeraX-PubChem: 2.0
    ChimeraX-Read-Pbonds: 1.0
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.0
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.2
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SeqView: 2.2
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.0
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.0
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.0.4
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.0
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.0
    ChimeraX-ToolshedUtils: 1.0
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.2.3
    ChimeraX-uniprot: 2.0
    ChimeraX-ViewDockX: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.3
    comtypes: 1.1.7
    cxservices: 1.0
    cycler: 0.10.0
    Cython: 0.29.20
    decorator: 4.4.2
    distlib: 0.3.1
    docutils: 0.16
    filelock: 3.0.12
    funcparserlib: 0.3.6
    gdcm: 2.8.8
    grako: 3.16.5
    h5py: 2.10.0
    html2text: 2020.1.16
    idna: 2.10
    ihm: 0.16
    imagecodecs: 2020.5.30
    imagecodecs-lite: 2020.1.31
    imagesize: 1.2.0
    ipykernel: 5.3.0
    ipython: 7.15.0
    ipython-genutils: 0.2.0
    jedi: 0.17.2
    Jinja2: 2.11.2
    jupyter-client: 6.1.3
    jupyter-core: 4.6.3
    kiwisolver: 1.2.0
    line-profiler: 2.1.2
    lxml: 4.5.1
    MarkupSafe: 1.1.1
    matplotlib: 3.2.1
    msgpack: 1.0.0
    netifaces: 0.10.9
    networkx: 2.4
    numexpr: 2.7.1
    numpy: 1.18.5+mkl
    numpydoc: 1.0.0
    openvr: 1.12.501
    packaging: 20.4
    parso: 0.7.1
    pickleshare: 0.7.5
    Pillow: 7.1.2
    pip: 20.2.2
    pkginfo: 1.5.0.1
    prompt-toolkit: 3.0.7
    psutil: 5.7.0
    pycollada: 0.7.1
    pydicom: 2.0.0
    Pygments: 2.6.1
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 2.4.7
    PyQt5-commercial: 5.12.3
    PyQt5-sip: 4.19.19
    PyQtWebEngine-commercial: 5.12.1
    python-dateutil: 2.8.1
    pytz: 2020.1
    pywin32: 228
    pyzmq: 19.0.2
    qtconsole: 4.7.4
    QtPy: 1.9.0
    RandomWords: 0.3.0
    requests: 2.24.0
    scipy: 1.4.1
    setuptools: 49.4.0
    sfftk-rw: 0.6.6.dev0
    six: 1.15.0
    snowballstemmer: 2.0.0
    sortedcontainers: 2.2.2
    Sphinx: 3.1.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 1.0.3
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.4
    suds-jurko: 0.6
    tables: 3.6.1
    tifffile: 2020.6.3
    tinyarray: 1.2.2
    tornado: 6.0.4
    traitlets: 5.0.4
    urllib3: 1.25.10
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.34.2
    WMI: 1.5.1
File attachment: PDBDEV_00000010.cif

PDBDEV_00000010.cif​

Attachments (1)

PDBDEV_00000010.cif​ (5.8 MB ) - added by 1449177995@… 5 years ago.
Added by email2trac

Change History (4)

by 1449177995@…, 5 years ago

Attachment: PDBDEV_00000010.cif​ added

Added by email2trac

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Input/Output
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → IHM: cached zip file corrupted

comment:2 by Tom Goddard, 5 years ago

Cc: ben@… added

I think your problem opening the IHM model 10 (nuclear pore) is that the first time you were fetching it the download was interrupted. The data is not just in the *.cif file -- that file also references various zip files that get downloaded separately and ChimeraX caches those. If ChimeraX caches a half downloaded zip file then it will fail to open. The zip files are hundreds of Mbytes for this structure so it can take quite a while to download.

The cached zip files are in ~/Downloads/ChimeraX/DOI. To fix the problem delete that DOI directory.

A better way to remedy this would be to use the ignoreCache option but apparently the code is ignoring that so it does not work in my test

open 10 from pdbdev ignoreCache true

Ideally ChimeraX would detect and delete half-downloaded files.

comment:3 by Tom Goddard, 5 years ago

Type: defect → enhancement

I will leave this bug report open, and hope in the future to improve the code to detect half-downloaded files and refetch them. Also should make the ignoreCache option work (it works for the *.cif file, but is ignored for fetching linked files mentioned in the .cif file).

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