Opened 7 years ago

Closed 7 years ago

#1680 closed defect (fixed)

Vseries save: No module named 'chimerax.core.commands.parse'

Reported by: matt.akamatsu@… 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:        Darwin-18.2.0-x86_64-i386-64bit
ChimeraX Version: 0.9 (2019-02-05)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
note | available bundle cache has not been initialized yet  
  
UCSF ChimeraX version: 0.9 (2019-02-05)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open "/Users/makamats/Documents/3I_LLSM_demo_working/AP2-rpc3 sample day 02
quad filter.sld - Arp2-rpc3 sample 03 dual color.Deskew.tif"

Opened multi-channel map AP2-rpc3 sample day 02 quad filter.sld - Arp2-rpc3
sample 03 dual color.Deskew.tif, 2 channels, grid size 768,1173,91, pixel
0.104,0.104,0.297, shown at step 2, values uint16  

> toolshed show '"Volume Viewer"'

> hide #!1.1 models

> show #!1.1 models

> hide #!1.1 models

> toolshed show '"Volume Viewer"'

> toolshed show '"Basic Actions"'

> save /Users/makamats/Desktop/image1.png supersample 3

> close session

> open "/Users/makamats/Documents/3I_LLSM_demo_working/AP2-rpc3 sample day 02
quad filter.sld - Arp2-rpc3 sample 03 dual color timelapse.Deskew.tif"

Opened AP2-rpc3 sample day 02 quad filter.sld - Arp2-rpc3 sample 03 dual color
timelapse.Deskew.tif, grid size 1173,768,1, pixel 1, shown at step 1, values
uint16  

> show target m

> view clip false

> view clip false

> close session

> close

> open /Users/makamats/Documents/3I_LLSM_demo_working/AP2-rpc3 sample day 02
quad filter.sld - Arp2-rpc3 sample 03 dual color timelapse.Deskew.tif

File not found: /Users/makamats/Documents/3I_LLSM_demo_working/AP2-rpc3  

> open
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/image_sequence/AP2-rpc3*.tif

Opened AP2-rpc3 sample day 02 quad filter.sld - Arp2-rpc3 sample 04 dual color
fast timelapse.Deskew_box1_t001_z001_c001.tif, grid size 461,274,9300, pixel
1, shown at step 1, values uint16  

> view clip false

> close

> open
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/image_sequence/AP2-rpc3*c001.tif

Opened AP2-rpc3 sample day 02 quad filter.sld - Arp2-rpc3 sample 04 dual color
fast timelapse.Deskew_box1_t001_z001_c001.tif, grid size 461,274,4650, pixel
1, shown at step 1, values uint16  

> open
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/image_sequence/AP2-rpc3*c002.tif

Opened AP2-rpc3 sample day 02 quad filter.sld - Arp2-rpc3 sample 04 dual color
fast timelapse.Deskew_box1_t001_z001_c002.tif, grid size 461,274,4650, pixel
1, shown at step 1, values uint16  

> show target m

> show #1 target m

> show #1 target m

> close

> open
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/Users/makamats/Documents/3I_LLSM_demo_working/analysis/pylattice_testData/10x10x10_developmentData/.h5

File not found:
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/Users/makamats/Documents/3I_LLSM_demo_working/analysis/pylattice_testData/10x10x10_developmentData/.h5  

> open
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/myData/.h5

File not found:
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/myData/.h5  
Traceback (most recent call last):  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 150, in undo  
inst.undo()  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 350, in undo  
self._update_owner(owner, attribute, old_value, option)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 379, in _update_owner  
setattr(owner, attribute, value)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 250, in _set_display  
Drawing.set_display(self, display)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 317, in set_display  
dp = empty((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
undo failed: object of type 'NoneType' has no len():  
TypeError: object of type 'NoneType' has no len()  
  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 317, in set_display  
dp = empty((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 150, in undo  
inst.undo()  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 350, in undo  
self._update_owner(owner, attribute, old_value, option)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/undo.py", line 379, in _update_owner  
setattr(owner, attribute, value)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 228, in __setattr__  
super(Drawing, self).__setattr__(key, value)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 250, in _set_display  
Drawing.set_display(self, display)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 317, in set_display  
dp = empty((len(self._positions),), bool)  
TypeError: object of type 'NoneType' has no len()  
  
undo failed: object of type 'NoneType' has no len():  
TypeError: object of type 'NoneType' has no len()  
  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/graphics/drawing.py", line 317, in set_display  
dp = empty((len(self._positions),), bool)  
  
See log for complete Python traceback.  
  

> open
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/myData:.h5

Traceback (most recent call last):  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 252, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2615, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 41, in open  
from_database=from_database, ignore_cache=ignore_cache, **kw))  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 117, in open  
models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
return f(*args, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 598, in open  
session, filenames, format=format, name=name, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 467, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 423, in open_data  
models, status = open_func(*args, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3474, in open_map_format  
return open_map(session, stream, name=name, format=format, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3076, in open_map  
verbose = kw.get('verbose'))  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 151, in open_file  
data = open_func(apath, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/emanhdf/eman_hdf_format.py", line 62, in __init__  
raise ValueError('EMAN HDF5 file %s contains no arrays' % path)  
ValueError: EMAN HDF5 file
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/myData:.h5
contains no arrays  
  
ValueError: EMAN HDF5 file
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/myData:.h5
contains no arrays  
  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/emanhdf/eman_hdf_format.py", line 62, in __init__  
raise ValueError('EMAN HDF5 file %s contains no arrays' % path)  
  
See log for complete Python traceback.  
  

> open
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/:Users:makamats:Documents:3I_LLSM_demo_working:analysis:pylattice_testData:10x10x10_developmentData:.h5

Traceback (most recent call last):  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 252, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2615, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 41, in open  
from_database=from_database, ignore_cache=ignore_cache, **kw))  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 117, in open  
models = handle_unknown_kw(session.models.open, paths, format=format,
name=name, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/open.py", line 62, in handle_unknown_kw  
return f(*args, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/models.py", line 598, in open  
session, filenames, format=format, name=name, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 467, in open_multiple_data  
models, status = open_data(session, fspec, format=format, name=name, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/io.py", line 423, in open_data  
models, status = open_func(*args, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3474, in open_map_format  
return open_map(session, stream, name=name, format=format, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/volume.py", line 3076, in open_map  
verbose = kw.get('verbose'))  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/fileformats.py", line 151, in open_file  
data = open_func(apath, **kw)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/emanhdf/__init__.py", line 18, in open  
return read_eman_hdf5(path)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/emanhdf/eman_hdf_grid.py", line 48, in
read_eman_hdf5  
d = EMAN_HDF_Data(path)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/emanhdf/eman_hdf_format.py", line 62, in __init__  
raise ValueError('EMAN HDF5 file %s contains no arrays' % path)  
ValueError: EMAN HDF5 file
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/:Users:makamats:Documents:3I_LLSM_demo_working:analysis:pylattice_testData:10x10x10_developmentData:.h5
contains no arrays  
  
ValueError: EMAN HDF5 file
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/:Users:makamats:Documents:3I_LLSM_demo_working:analysis:pylattice_testData:10x10x10_developmentData:.h5
contains no arrays  
  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/data/emanhdf/eman_hdf_format.py", line 62, in __init__  
raise ValueError('EMAN HDF5 file %s contains no arrays' % path)  
  
See log for complete Python traceback.  
  

> close

> open
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/C2-AP2-rpc3
sample day 02 quad filter.sld - Arp2-rpc3 sample 04 dual color fast
timelapse.Deskew_box1.tif

File not found:
/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/C2-AP2-rpc3  

> open
"/Users/makamats/Documents/3I_LLSM_demo_working/analysis/stack_sequence/C2-AP2-rpc3
sample day 02 quad filter.sld - Arp2-rpc3 sample 04 dual color fast
timelapse.Deskew_box1.tif"

Opened map series C2-AP2-rpc3 sample day 02 quad filter.sld - Arp2-rpc3 sample
04 dual color fast timelapse.Deskew_box1.tif, 150 images, grid size
461,274,31, pixel 0.104,0.104,0.297, shown at step 1, values uint16  

> close

> open "/Users/makamats/Documents/3I_LLSM_demo_working/AP2-rpc3 sample day 02
quad filter.sld - Arp2-rpc3 sample 04 dual color fast
timelapse.Deskew_box1.tif"

Opened multichannel map series AP2-rpc3 sample day 02 quad filter.sld -
Arp2-rpc3 sample 04 dual color fast timelapse.Deskew_box1.tif, 2 channels, 150
images per channel, grid size 461,274,31, pixel 0.104,0.104,0.297, shown at
step 1, values uint16  

Missing or invalid "series" argument: invalid map series specifier  

> vseries save #1 "'/Users/makamats/Documents/3I_LLSM_demo_working/AP2-rpc3
sample day 02 quad filter.sld - Arp2-rpc3 sample 04 dual color fast
timelapse.Deskew_box1_ch0.cmap'"

Traceback (most recent call last):  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/cmd_line/tool.py", line 252, in execute  
cmd.run(cmd_text)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2615, in run  
result = ci.function(session, **kw_args)  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/series/vseries_command.py", line 183, in vseries_save  
from chimerax.core.commands.parse import CommandError  
ModuleNotFoundError: No module named 'chimerax.core.commands.parse'  
  
ModuleNotFoundError: No module named 'chimerax.core.commands.parse'  
  
File
"/private/var/folders/3y/bljtm6zd0wd14g_yc50sjwlw0000gn/T/AppTranslocation/065667D8-43D3-46A5-9556-72D09E050683/d/ChimeraX.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/series/vseries_command.py", line 183, in vseries_save  
from chimerax.core.commands.parse import CommandError  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 ATI-2.4.9
OpenGL renderer: AMD Radeon Pro 560X OpenGL Engine
OpenGL vendor: ATI Technologies Inc.

Change History (2)

comment:1 by Eric Pettersen, 7 years ago

Component: Unassigned → Volume Data
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Vseries save: No module named 'chimerax.core.commands.parse'

comment:2 by Tom Goddard, 7 years ago

Resolution: → fixed
Status: assigned → closed

Fixed in tonight's builds.

The vseries save command when given two or more series was trying to report an error that it can only handle one series, but reporting the error caused another error because of some moved code.

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