Opened 4 years ago

Closed 4 years ago

Last modified 4 years ago

#5892 closed defect (fixed)

Failure reading IMOD file

Reported by: wanda.kukulski@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Volume Data Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
In a first instance,  the attached imod model did open in chimeraX.  But when I added another object to it in imod,  the chimeraX failed to open it,  even when the second object was not present in the .mod file anymore (as in the attached file,  which is the one that generated the reported log).  The problem was the same in an older ChimeraX version (1.2.5). Best wishes and many thanks,  Wanda 

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim/TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim_Apaf1_segmentation2.mod

Read IMOD model
/Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
filt_fullrotxtrim1_bin2_3dmedian5_trim/TS1_dose-
filt_fullrotxtrim1_bin2_3dmedian5_trim_Apaf1_segmentation2.mod, pixel size
0.9496  

> open
> /Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim/TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim_Apaf1_segmentation2.mod format imod

Read IMOD model
/Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
filt_fullrotxtrim1_bin2_3dmedian5_trim/TS1_dose-
filt_fullrotxtrim1_bin2_3dmedian5_trim_Apaf1_segmentation2.mod, pixel size
0.9496, 1 surfaces  

> close

> open
> /Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim/TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim_Apaf1_segmentation2.mod format imod

Traceback (most recent call last):  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 333, in interceptRequest  
self._callback(info)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 92, in _intercept  
return interceptor(request_info, *args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 366, in intercept  
chimerax_intercept(*args, view=view, session=session)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 468, in chimerax_intercept  
session.ui.thread_safe(defer, session, qurl.url(no_formatting), from_dir)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 382, in thread_safe  
func(*args, **kw)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 459, in defer  
cxcmd(session, topic)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/htmlview.py", line 477, in cxcmd  
run(session, cmd)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/__init__.py", line 25, in open  
return imod.read_imod_model(session, path,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 6, in read_imod_model  
clist = read_imod(path)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 32, in read_imod  
clist = read_imod_chunks(f)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 52, in read_imod_chunks  
h = read_chunk(file, cformat)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 81, in read_chunk  
a = read_values(vtype, count, file)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
  
See log for complete Python traceback.  
  

> open
> /Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim/test2.mod

Traceback (most recent call last):  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/__init__.py", line 25, in open  
return imod.read_imod_model(session, path,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 6, in read_imod_model  
clist = read_imod(path)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 32, in read_imod  
clist = read_imod_chunks(f)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 52, in read_imod_chunks  
h = read_chunk(file, cformat)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 81, in read_chunk  
a = read_values(vtype, count, file)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
  
See log for complete Python traceback.  
  

> open
> /Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim/test3.mod

Traceback (most recent call last):  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/__init__.py", line 25, in open  
return imod.read_imod_model(session, path,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 6, in read_imod_model  
clist = read_imod(path)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 32, in read_imod  
clist = read_imod_chunks(f)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 52, in read_imod_chunks  
h = read_chunk(file, cformat)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 81, in read_chunk  
a = read_values(vtype, count, file)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
  
See log for complete Python traceback.  
  

> open
> /Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim/test3.mod

Traceback (most recent call last):  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/__init__.py", line 25, in open  
return imod.read_imod_model(session, path,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 6, in read_imod_model  
clist = read_imod(path)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 32, in read_imod  
clist = read_imod_chunks(f)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 52, in read_imod_chunks  
h = read_chunk(file, cformat)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 81, in read_chunk  
a = read_values(vtype, count, file)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
  
See log for complete Python traceback.  
  

> open
> /Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim/test3.mod

Traceback (most recent call last):  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 267, in event  
_open_dropped_file(self.session, event.file())  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1919, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/__init__.py", line 25, in open  
return imod.read_imod_model(session, path,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 6, in read_imod_model  
clist = read_imod(path)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 32, in read_imod  
clist = read_imod_chunks(f)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 52, in read_imod_chunks  
h = read_chunk(file, cformat)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 81, in read_chunk  
a = read_values(vtype, count, file)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
  
See log for complete Python traceback.  
  

> open
> /Users/kukulski/Projects/Project_Apaf1_ALICIA/CryoCLEM_cellopening_Dec2020_WD40KO/Krios1/models_TS1_dose-
> filt_fullrotxtrim1_bin2_3dmedian5_trim/test3.mod

Traceback (most recent call last):  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 267, in event  
_open_dropped_file(self.session, event.file())  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1919, in _open_dropped_file  
run(session, 'open %s' % FileNameArg.unparse(path))  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/__init__.py", line 25, in open  
return imod.read_imod_model(session, path,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 6, in read_imod_model  
clist = read_imod(path)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 32, in read_imod  
clist = read_imod_chunks(f)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 52, in read_imod_chunks  
h = read_chunk(file, cformat)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 81, in read_chunk  
a = read_values(vtype, count, file)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
  
See log for complete Python traceback.  
  

> open /Users/kukulski/Desktop/test3.mod

Traceback (most recent call last):  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/dialog.py", line 155, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 118, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 181, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 432, in collated_open  
return remember_data_format()  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/open_command/cmd.py", line 403, in remember_data_format  
models, status = func(*func_args, **func_kw)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/__init__.py", line 25, in open  
return imod.read_imod_model(session, path,  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 6, in read_imod_model  
clist = read_imod(path)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 32, in read_imod  
clist = read_imod_chunks(f)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 52, in read_imod_chunks  
h = read_chunk(file, cformat)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 81, in read_chunk  
a = read_values(vtype, count, file)  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
SyntaxError: Failed reading 16777216 bytes from IMOD file  
  
File
"/private/var/folders/k5/j559b8f924n46st30c5y5m800000gp/T/AppTranslocation/F0864245-54CF-4334-BD56-D5F55D6B5E0E/d/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/imod/imod.py", line 99, in read_values  
raise SyntaxError('Failed reading %d bytes from IMOD file' % bytes)  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-16.5.2
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics OpenGL Engine
OpenGL vendor: Intel Inc.Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro16,2
      Processor Name: Quad-Core Intel Core i5
      Processor Speed: 2 GHz
      Number of Processors: 1
      Total Number of Cores: 4
      L2 Cache (per Core): 512 KB
      L3 Cache: 6 MB
      Hyper-Threading Technology: Enabled
      Memory: 16 GB
      System Firmware Version: 1554.140.20.0.0 (iBridge: 18.16.14759.0.1,0)

Software:

    System Software Overview:

      System Version: macOS 11.5.1 (20G80)
      Kernel Version: Darwin 20.6.0
      Time since boot: 12 days 16:15

Graphics/Displays:

    Intel Iris Plus Graphics:

      Chipset Model: Intel Iris Plus Graphics
      Type: GPU
      Bus: Built-In
      VRAM (Dynamic, Max): 1536 MB
      Vendor: Intel
      Device ID: 0x8a53
      Revision ID: 0x0007
      Metal Family: Supported, Metal GPUFamily macOS 2
      Displays:
        PHL 329P9:
          Resolution: 6016 x 3384
          UI Looks like: 3008 x 1692 @ 60.00Hz
          Framebuffer Depth: 30-Bit Color (ARGB2101010)
          Display Serial Number: UHB2008002442
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
          Connection Type: Thunderbolt/DisplayPort

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0
File attachment: test3.mod

test3.mod​

Attachments (3)

test3.mod​ (73.7 KB ) - added by wanda.kukulski@… 4 years ago.
Added by email2trac
G4_R1_TS1_ro_mode1trim_median3px_vesicles1.mod​ (23.5 KB ) - added by wanda.kukulski@… 4 years ago.
Added by email2trac
test3-1.mod​ (73.7 KB ) - added by wanda.kukulski@… 4 years ago.
Added by email2trac

Download all attachments as: .zip

Change History (10)

by wanda.kukulski@…, 4 years ago

Attachment: test3.mod​ added

Added by email2trac

comment:1 by Eric Pettersen, 4 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Failure reading IMOD file

comment:2 by Tom Goddard, 4 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in tonight's ChimeraX daily builds.

ChimeraX was not correctly reading four IMOD file records MOST, OBST, COST, MEST if there were multiple objects. Those records are variable length depending on the number of objects and ChimeraX believed they were fixed length. Since the ChimeraX code does not use those records I made it skip them since it would be a bit of work to make the code handle the variable record size. I am not sure why IMOD is still including multiple object info into the file if you delete the second object. At any rate, ChimeraX has read the files ok for the past 10 years I guess because almost no files have the multi-object records that cause the problem. Possibly your use of IMOD was somewhat unusual and resulted in these records that ChimeraX did not read correctly.

in reply to:  4 comment:3 by goddard@…, 4 years ago 

Here are the IMOD file format docs describing the records.

https://bio3d.colorado.edu/imod/doc/binspec.html

in reply to:  5 ; comment:4 by wanda.kukulski@…, 4 years ago 

Dear ChimeraX team,
Dear Tom,

Thank you very much for dealing with this so quickly! I have just today downloaded the daily build 1.4.dev202201082018 (2022-01-08) but unfortunately the problem seems to persist with the file test3.mod which I attach again. Am I supposed to change something in the settings? Interestingly, I also have examples of imod files with multiple objects which have been in the past read by ChimeraX without problem. I  attach one such example (file name ending with vesicles1.mod).

I also want to use this opportunity to say a huge THANK YOU to your team for developing ChimeraX; it is just fantastic in so many ways for us in the tomography field. One way we use it is that we do segmentation models in IMOD followed by rendering and presentation of the scenes in ChimeraX, which results in figures and movies of simply unmatched quality. Thank you all so much.

Best wishes
Wanda


----------------------------------------------------------------
Wanda Kukulski
Institute of Biochemistry and Molecular Medicine
University of Bern
Bühlstrasse 28
3012 Bern
Switzerland
phone: +41 31 684 41 29





On 11 Jan 2022, at 00:15, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#5892: Failure reading IMOD file
---------------------------------------+-------------------------
         Reporter:  wanda.kukulski@…  |      Owner:  Tom Goddard
             Type:  defect            |     Status:  closed
         Priority:  normal            |  Milestone:
        Component:  Volume Data       |    Version:
       Resolution:  fixed             |   Keywords:
       Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
          Project:  ChimeraX          |
---------------------------------------+-------------------------
Changes (by Tom Goddard):

* status:  assigned => closed
* resolution:   => fixed


Comment:

Fixed in tonight's ChimeraX daily builds.

ChimeraX was not correctly reading four IMOD file records MOST, OBST,
COST, MEST if there were multiple objects.  Those records are variable
length depending on the number of objects and ChimeraX believed they were
fixed length.  Since the ChimeraX code does not use those records I made
it skip them since it would be a bit of work to make the code handle the
variable record size.  I am not sure why IMOD is still including multiple
object info into the file if you delete the second object.  At any rate,
ChimeraX has read the files ok for the past 10 years I guess because
almost no files have the multi-object records that cause the problem.
Possibly your use of IMOD was somewhat unusual and resulted in these
records that ChimeraX did not read correctly.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5892#comment:2>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
ChimeraX Issue Tracker

G4_R1_TS1_ro_mode1trim_median3px_vesicles1.mod​

test3-1.mod​

by wanda.kukulski@…, 4 years ago

Attachment: G4_R1_TS1_ro_mode1trim_median3px_vesicles1.mod​ added

Added by email2trac

by wanda.kukulski@…, 4 years ago

Attachment: test3-1.mod​ added

Added by email2trac

in reply to:  8 ; comment:5 by goddard@…, 4 years ago 

The daily builds failed last night so you don’t have the fixed ChimeraX.  The daily build you downloaded has the date Jan 8 in the file name and the fix went in Jan 10.  We should get tonights builds working which would run about 4 AM California time.

comment:6 by Tom Goddard, 4 years ago

Hi Wanda,

Glad you have been making good use of ChimeraX for looking at IMOD segmentations of EM tomography. The reason your test3.mod file fails to open is because IMOD put a MOST record in the file for multiple objects. Your ...vesicles1.mod file does not have any MOST record. I don't know exactly why IMOD sometimes writes this and sometimes does not. But looking at the IMOD file documentation about the MOST record ​https://bio3d.colorado.edu/imod/doc/binspec.html it looks like it may be added because you changed some default settings. Here is some of the description

MOST  General storage information for model.    (Variable size) 
OBST  General storage information for object.    (Variable size) 
COST  General storage information for contour.    (Variable size) 
MEST  General storage information for mesh.    (Variable size) 
These chunks contain extra information for their respective entities. They were designed to hold fine-grained display properties for objects, contours, and meshes, but could be used for any kind of additional information that will fit in the Store data structure. The chunk consists of a series of Store entries, each 12 bytes long:
Length Type     Name    Description
-------------------------------------------------------------------
2      short    type    Type of information.  Currently defined types are:
                          1  Color change
                          2  Fill color change
                          3  Transparency change
                          4  Do not connect to next point or do not display
                          5  A connection number for meshing
                          6  3D line width change
                          7  2D line width change
                          8  Symbol type
                          9  Symbol size
                          10 General floating point value
                          11 Min and max of general values
...

I can tell you how to modify your current ChimeraX to fix this problem if you do not want to wait for the daily build. Edit the ChimeraX file

ChimeraX-1.3.app/Contents/lib/python3.9/site-packages/chimerax/imod/imod_spec.py

changing the line near the bottom of the file

    b'MOST': most_format,

to

#    b'MOST': most_format,

then restart ChimeraX and it will load test3.mod. Make sure to save the file as plain text.

in reply to:  10 comment:7 by wanda.kukulski@…, 4 years ago 

Dear Tom,

Thank you so much! I’m sorry if I appeared impatient; somehow I didn’t realise yesterday wasn’t the 8th… Of course there’s no rush and I’m actually surprised how quickly you deal with my questions.

Thanks also for looking into the difference between the two .mod files! That’s really very helpful. I haven’t found yet what setting I could have changed but I will keep looking. In any case, the solution to not read the MOST record in ChimeraX seems most pragmatic! Thanks a lot for your help!!

Best wishes
Wanda

----------------------------------------------------------------
Wanda Kukulski
Institute of Biochemistry and Molecular Medicine
University of Bern
Bühlstrasse 28
3012 Bern
Switzerland
phone: +41 31 684 41 29



On 11 Jan 2022, at 19:29, ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu<mailto:ChimeraX-bugs-admin@cgl.ucsf.edu>> wrote:

#5892: Failure reading IMOD file
---------------------------------------+-------------------------
         Reporter:  wanda.kukulski@…  |      Owner:  Tom Goddard
             Type:  defect            |     Status:  closed
         Priority:  normal            |  Milestone:
        Component:  Volume Data       |    Version:
       Resolution:  fixed             |   Keywords:
       Blocked By:                    |   Blocking:
Notify when closed:                    |   Platform:  all
          Project:  ChimeraX          |
---------------------------------------+-------------------------

Comment (by Tom Goddard):

Hi Wanda,

  Glad you have been making good use of ChimeraX for looking at IMOD
segmentations of EM tomography.  The reason your test3.mod file fails to
open is because IMOD put a MOST record in the file for multiple objects.
Your ...vesicles1.mod file does not have any MOST record.  I don't know
exactly why IMOD sometimes writes this and sometimes does not.  But
looking at the IMOD file documentation about the MOST record
https://bio3d.colorado.edu/imod/doc/binspec.html it looks like it may be
added because you changed some default settings.  Here is some of the
description


{{{
MOST  General storage information for model.    (Variable size)
OBST  General storage information for object.    (Variable size)
COST  General storage information for contour.    (Variable size)
MEST  General storage information for mesh.    (Variable size)
These chunks contain extra information for their respective entities. They
were designed to hold fine-grained display properties for objects,
contours, and meshes, but could be used for any kind of additional
information that will fit in the Store data structure. The chunk consists
of a series of Store entries, each 12 bytes long:
Length Type     Name    Description
-------------------------------------------------------------------
2      short    type    Type of information.  Currently defined types are:
                          1  Color change
                          2  Fill color change
                          3  Transparency change
                          4  Do not connect to next point or do not
display
                          5  A connection number for meshing
                          6  3D line width change
                          7  2D line width change
                          8  Symbol type
                          9  Symbol size
                          10 General floating point value
                          11 Min and max of general values
...
}}}


I can tell you how to modify your current ChimeraX to fix this problem if
you do not want to wait for the daily build.  Edit the ChimeraX file

{{{
ChimeraX-1.3.app/Contents/lib/python3.9/site-
packages/chimerax/imod/imod_spec.py
}}}

changing the line near the bottom of the file

{{{
    b'MOST': most_format,
}}}

to

{{{
#    b'MOST': most_format,
}}}

then restart ChimeraX and it will load test3.mod.  Make sure to save the
file as plain text.

--
Ticket URL: <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/5892#comment:6>
ChimeraX <https://www.rbvi.ucsf.edu/chimerax/>
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