id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2761 mmCIF fetch: Compressed file ended before the end-of-stream marker was reached chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.2.0-x86_64-i386-64bit ChimeraX Version: 0.92 (2020-01-04) Description (Describe the actions that caused this problem to occur here) Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 0.92 (2020-01-04) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > help help:user > open 6n2y Summary of feedback from opening 6n2y fetched from pdb --- note | Fetching compressed mmCIF 6n2y from http://files.rcsb.org/download/6n2y.cif Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/gui.py"", line 600, in customEvent func(*args, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py"", line 345, in defer cxcmd(session, topic) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/ui/widgets/htmlview.py"", line 464, in cxcmd run(session, cmd) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/run.py"", line 31, in run results = command.run(text, log=log) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/cli.py"", line 2837, in run result = ci.function(session, **kw_args) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 44, in open db_models, status = _fetch_from_database(session, db_id, db_name, db_format, name, ignore_cache, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/commands/open.py"", line 153, in _fetch_from_database ignore_cache=ignore_cache, **kw) File ""/Applications/ChimeraX_Daily.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 ""/Applications/ChimeraX_Daily.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 ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/toolshed/info.py"", line 383, in fetch_cb return fetch_shim(session, identifier, **kw) File ""/Applications/ChimeraX_Daily.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 ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/__init__.py"", line 46, in fetch_from_database return fetcher(session, identifier, ignore_cache=ignore_cache, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/atomic/mmcif/mmcif.py"", line 315, in fetch_mmcif cache, ignore_cache=ignore_cache) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/fetch.py"", line 69, in fetch_file check_certificates=check_certificates, name=name, timeout=timeout) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/fetch.py"", line 164, in retrieve_url read_and_uncompress(response, f, name, content_length, logger) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/fetch.py"", line 194, in read_and_uncompress shutil.copyfileobj(uncompressed, file_out) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/shutil.py"", line 79, in copyfileobj buf = fsrc.read(length) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py"", line 276, in read return self._buffer.read(size) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/_compression.py"", line 68, in readinto data = self.read(len(byte_view)) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py"", line 482, in read raise EOFError(""Compressed file ended before the "" EOFError: Compressed file ended before the end-of-stream marker was reached EOFError: Compressed file ended before the end-of-stream marker was reached File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/gzip.py"", line 482, in read raise EOFError(""Compressed file ended before the "" See log for complete Python traceback. OpenGL version: 4.1 INTEL-14.3.9 OpenGL renderer: Intel(R) HD Graphics 5300 OpenGL vendor: Intel Inc. }}} " defect closed normal Input/Output fixed Greg Couch all ChimeraX