id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 1398 Open pdbdev 10: File is not a zip file mr.edvinas.stankunas@… Tom Goddard "{{{ 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 }}} " defect closed normal Higher-Order Structure can't reproduce all ChimeraX