id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 2668 RFE: open compressed maps directly lpravda@… Tom Goddard "{{{ The following bug report has been submitted: Platform: Darwin-19.0.0-x86_64-i386-64bit ChimeraX Version: 0.91 (2019-12-05) Description I tried opening compressed EMDB map downloaded from ftp://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-2752/map/emd_2752.map.gz. Although opening decompressed map works, I think allowing opening compressed maps would be very usefull functionality as well (if this is presently unsupported) Log: UCSF ChimeraX version: 0.91 (2019-12-05) © 2016-2019 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX > open /Users/lpravda/Downloads/emd_2752.map.gz Traceback (most recent call last): File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/fileformats.py"", line 157, in open_file data.extend(open_func(p, **kw)) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/ccp4/__init__.py"", line 18, in open return [CCP4Grid(path)] File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/ccp4/ccp4_grid.py"", line 21, in __init__ MRCGrid.__init__(self, path, file_type = 'ccp4') File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/mrc/mrc_grid.py"", line 24, in __init__ d = mrc_format.MRC_Data(path, file_type) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/mrc/mrc_format.py"", line 43, in __init__ v = self.read_header_values(file, file_size, file_type) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/mrc/mrc_format.py"", line 189, in read_header_values % v['nsymbt'])) File """", line None SyntaxError: MRC header value nsymbt (-1248613872) is invalid During handling of the above exception, another exception occurred: 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 628, in _qt_safe run(session, ""open "" + "" "".join([FileNameArg.unparse(p) for p in paths])) 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 68, in open path_models = session.models.open(paths, format=format, name=name, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/models.py"", line 700, in open session, filenames, format=format, name=name, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/core/io.py"", line 485, in open_multiple_data models, status = open_func(session, paths, mname, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 3610, in open_map_format return open_map(session, path, name=name, format=format, **kw) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/volume.py"", line 3209, in open_map verbose = kw.get('verbose')) File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/fileformats.py"", line 159, in open_file raise FileFormatError(value) chimerax.map.data.fileformats.FileFormatError: MRC header value nsymbt (-1248613872) is invalid chimerax.map.data.fileformats.FileFormatError: MRC header value nsymbt (-1248613872) is invalid File ""/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site- packages/chimerax/map/data/fileformats.py"", line 159, in open_file raise FileFormatError(value) See log for complete Python traceback. OpenGL version: 4.1 ATI-3.2.24 OpenGL renderer: AMD Radeon Pro 560 OpenGL Engine OpenGL vendor: ATI Technologies Inc. }}} " enhancement assigned normal Volume Data Elaine Meng all ChimeraX