MRC header value nsymbt is invalid

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-17.3.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-06-06)
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: 0.9 (2019-06-06)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
/Users/IB_office_computer/Documents/grant_award_application/NIH_R01/Oct2019/figures/cryo-
EM_maps/volume_398_1.mrc

Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 155, in open_file  
data.extend(open_func(p, **kw))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/mrc/__init__.py", line 24, in open  
return [MRCGrid(path)]  
File
"/Applications/ChimeraX-0.9.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-0.9.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-0.9.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 "<string>", line None  
SyntaxError: MRC header value nsymbt (-1798955944) is invalid  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 141, in <lambda>  
lambda e, what=what, self=self: self.handle_scheme(what),  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/toolbar/tool.py", line 96, in handle_scheme  
run(self.session, f'{value}')  
File
"/Applications/ChimeraX-0.9.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-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
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 64, in open  
path_models = session.models.open(paths, format=format, name=name, **kw)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 601, in open  
session, filenames, format=format, name=name, **kw)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 473, in open_multiple_data  
models, status = open_func(session, paths, mname, **kw)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3584, in open_map_format  
return open_map(session, path, name=name, format=format, **kw)  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3186, in open_map  
verbose = kw.get('verbose'))  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 157, in open_file  
raise FileFormatError(value)  
chimerax.map.data.fileformats.FileFormatError: MRC header value nsymbt
(-1798955944) is invalid  
  
chimerax.map.data.fileformats.FileFormatError: MRC header value nsymbt
(-1798955944) is invalid  
  
File
"/Applications/ChimeraX-0.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 157, in open_file  
raise FileFormatError(value)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-1.60.24
OpenGL renderer: AMD Radeon Pro 450 OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

[Tom Goddard]

As the error message says the MRC header has an invalid value for nsymbt. This value indicates how many extra bytes are after the header before the data, so not having a correct value means it is not possible to find where the map data begins. Probably the correct value is 0. Whatever program wrote the file must have used an uninitialized nsymbt value.