Opened 5 years ago

Closed 5 years ago

#3389 closed defect (nonchimerax)

MRC file: file size too small for grid size

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version: 0.91
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Linux-3.10.0-957.el7.x86_64-x86_64-with-centos-7.6.1810-Core
ChimeraX Version: 0.91 (2019-12-23)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Errors  
---  
error | ChimeraX requires OpenGL graphics version 3.3.  
Your computer graphics driver provided version 2.1  
Try updating your graphics driver.  
warning | No statusbar messages will be shown due to inadequate OpenGL  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.91 (2019-12-23)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /home/xiao/18/STRUCTURES/quxiao/pH7.4_echo18_FcRn.mrc

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 157, in open_file  
data.extend(open_func(p, **kw))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/mrc/__init__.py", line 24, in open  
return [MRCGrid(path)]  
File "/opt/UCSF/ChimeraX/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/mrc/mrc_format.py", line 51, in __init__  
self.check_header_values(v, file_size, file)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/mrc/mrc_format.py", line 245, in
check_header_values  
raise SyntaxError(msg)  
File "<string>", line None  
SyntaxError: File size 300744704 too small for grid size (432,432,432)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py",
line 723, in open  
session, filenames, format=format, name=name, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/io.py",
line 499, in open_multiple_data  
models, status = open_func(session, paths, mname, **kw)  
File "/opt/UCSF/ChimeraX/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
line 3209, in open_map  
verbose = kw.get('verbose'))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 159, in open_file  
raise FileFormatError(value)  
chimerax.map.data.fileformats.FileFormatError: File size 300744704 too small
for grid size (432,432,432)  
  
chimerax.map.data.fileformats.FileFormatError: File size 300744704 too small
for grid size (432,432,432)  
  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 159, in open_file  
raise FileFormatError(value)  
  
See log for complete Python traceback.  
  

> open /home/xiao/18/STRUCTURES/quxiao/pH7.4_echo18_FcRn.mrc

Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 157, in open_file  
data.extend(open_func(p, **kw))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/mrc/__init__.py", line 24, in open  
return [MRCGrid(path)]  
File "/opt/UCSF/ChimeraX/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/mrc/mrc_format.py", line 51, in __init__  
self.check_header_values(v, file_size, file)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/mrc/mrc_format.py", line 245, in
check_header_values  
raise SyntaxError(msg)  
File "<string>", line None  
SyntaxError: File size 300744704 too small for grid size (432,432,432)  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "/opt/UCSF/ChimeraX/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2837, in run  
result = ci.function(session, **kw_args)  
File "/opt/UCSF/ChimeraX/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/models.py",
line 723, in open  
session, filenames, format=format, name=name, **kw)  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/core/io.py",
line 499, in open_multiple_data  
models, status = open_func(session, paths, mname, **kw)  
File "/opt/UCSF/ChimeraX/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 "/opt/UCSF/ChimeraX/lib/python3.7/site-packages/chimerax/map/volume.py",
line 3209, in open_map  
verbose = kw.get('verbose'))  
File "/opt/UCSF/ChimeraX/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 159, in open_file  
raise FileFormatError(value)  
chimerax.map.data.fileformats.FileFormatError: File size 300744704 too small
for grid size (432,432,432)  
  
chimerax.map.data.fileformats.FileFormatError: File size 300744704 too small
for grid size (432,432,432)  
  
File "/opt/UCSF/ChimeraX/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: unknown
Could not make opengl context current

Change History (2)

comment:1 by Eric Pettersen, 5 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → MRC file: file size too small for grid size
Version: → 0.91

comment:2 by Tom Goddard, 5 years ago

Resolution: → nonchimerax
Status: assigned → closed

This user has no luck. There graphics provides only OpenGL 2.1 so nothing will display and their data file is truncated.

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