id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 5892 Failure reading IMOD file wanda.kukulski@… Tom Goddard "{{{ 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 }}} [attachment:""test3.mod""] " defect closed normal Volume Data fixed all ChimeraX