id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2224 Problem opening various PDBDEV files: File is not a zip file benoit.palancade@… Tom Goddard "{{{ 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. }}} " defect closed normal Input/Output nonchimerax ben@… brinda.vallat@… all ChimeraX