open 0069 fromDatabase emdb: MRC file is truncated

[maria.anastasina@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.15063
ChimeraX Version: 0.91 (2019-09-07)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-09-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 0069 fromDatabase emdb

Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\fileformats.py", line 151, in open_file  
data = open_func(apath, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\ccp4\\__init__.py", line 18, in open  
return [CCP4Grid(path)]  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\ccp4\ccp4_grid.py", line 21, in __init__  
MRCGrid.__init__(self, path, file_type = 'ccp4')  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\mrc\mrc_grid.py", line 24, in __init__  
d = mrc_format.MRC_Data(path, file_type)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\mrc\mrc_format.py", line 39, in __init__  
nc = self.read_values(file, int32, 1)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\mrc\mrc_format.py", line 256, in read_values  
% (count, etype.__name__)))  
File "<string>", line None  
SyntaxError: MRC file is truncated. Failed reading 1 values, type int32  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\cmd_line\tool.py", line 254, in execute  
cmd.run(cmd_text)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2688, in run  
result = ci.function(session, **kw_args)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\open.py", line 148, in _fetch_from_database  
ignore_cache=ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\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 "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\fetch.py",
line 497, in fetch  
return fetch(session, database_id, ignore_cache=ignore_cache, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\emdb_fetch.py", line 48, in fetch_emdb  
models, status = io.open_data(session, filename, format = 'ccp4', name =
emdb_id, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\core\io.py",
line 435, in open_data  
models, status = open_func(*args, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 3598, in open_map_format  
return open_map(session, path, name=name, format=format, **kw)  
File "C:\Program Files\ChimeraX\bin\lib\site-packages\chimerax\map\volume.py",
line 3197, in open_map  
verbose = kw.get('verbose'))  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\fileformats.py", line 157, in open_file  
raise FileFormatError(value)  
chimerax.map.data.fileformats.FileFormatError: MRC file is truncated. Failed
reading 1 values, type int32  
  
chimerax.map.data.fileformats.FileFormatError: MRC file is truncated. Failed
reading 1 values, type int32  
  
File "C:\Program Files\ChimeraX\bin\lib\site-
packages\chimerax\map\data\fileformats.py", line 157, in open_file  
raise FileFormatError(value)  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 NVIDIA 417.71
OpenGL renderer: Quadro P4000/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation

[Tom Goddard]

As the error message says, the MRC file was truncated. In fact I can tell by where it failed reading the file that it had size 0. Possibly you quit ChimeraX while it was fetching this file before the fetch finished, or maybe EMDB gave you a 0 length file because it was in the process of updating. This EMDB entry fetches fine for me.

Now you probably have the size 0 file cached, because ChimeraX caches the downloaded files

~/Downloads/ChimeraX/EMDB/emd_0069.map

You can delete that file, or you can use

open 0069 from emdb ignorecache true

to get a new copy of the file.