Opened 2 years ago

Closed 2 years ago

#9489 closed defect (fixed)

Collada not saved in session

Reported by: phil.cruz@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Sessions Version:
Keywords: Cc: Zach Pearson
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-12.6.7-arm64-arm-64bit
ChimeraX Version: 1.7.dev202307280011 (2023-07-28 00:11:13 UTC)
Description
This session in the attachment was saved with a dicom in #1 and two dae files loaded in #2 and #3. Opening the cxs file loads the dicom, and the dae files appear in #2 and #3 in the model panel, but the dae models are not loaded. Need to be able to save the aligned dae and restore it in the session. All files are in the attached zip. 
This session in the attachment was saved with a dicom in #1 and two dae files loaded in #2 and #3. Opening the cxs file loads the dicom, and the dae files appear in #2 and #3 in the model panel, but the dae models are not loaded. Need to be able to save the aligned dae and restore it in the session. All files are in the attached zip.  

Log:
UCSF ChimeraX version: 1.7.dev202307280011 (2023-07-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/cruzp2/Desktop/minipig-dicom-zip/minipig_test_what_is
> saved3.cxs"

Opened 4 CT () as #1.1.1, grid size 512,512,178, pixel 0.545,0.545,2.98, shown
at step 1, values float32  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

Log from Fri Jul 28 14:44:05 2023UCSF ChimeraX version: 1.7.dev202307280011
(2023-07-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/cruzp2/Desktop/minipig_test_what_is saved2.cxs" format session

Opened 4 CT () as #1.1.1, grid size 512,512,178, pixel 0.545,0.545,2.98, shown
at step 1, values float32  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

Log from Fri Jul 28 14:39:37 2023UCSF ChimeraX version: 1.7.dev202307280011
(2023-07-28)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/minipig-dicom_2.cxs format session

Opened 4 CT () as #1.1.1, grid size 512,512,178, pixel 0.545,0.545,2.98, shown
at step 1, values float32  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

dlopen(/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openvr/libopenvr_api_32.dylib, 0x0006): tried:
'/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/openvr/libopenvr_api_32.dylib' (mach-o file, but is an incompatible
architecture (have (x86_64), need (arm64e)))  

restore_snapshot for "SteamVRCamera" returned None  

Log from Fri Jul 28 14:14:40 2023UCSF ChimeraX version: 1.7.dev202307180036
(2023-07-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open "/Users/cruzp2/Desktop/minipig_test_what_is saved.cxs"

Opened 4 CT () as #1.1.1, grid size 512,512,178, pixel 0.545,0.545,2.98, shown
at step 1, values float32  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

Log from Fri Jul 28 11:52:39 2023UCSF ChimeraX version: 1.7.dev202307180036
(2023-07-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/minipig-dicom.cxs

Opened 4 CT () as #1.1.1, grid size 512,512,178, pixel 0.545,0.545,2.98, shown
at step 1, values float32  

restore_snapshot for "Volume" returned None  

restore_snapshot for "VolumeImage" returned None  

Log from Fri Jul 28 09:59:59 2023UCSF ChimeraX version: 1.7.dev202307180036
(2023-07-18)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Public/AFRRI/D008.dae

Traceback (most recent call last):  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/__init__.py", line 129, in open  
return collada.read_collada_surfaces(session, data, file_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 21, in read_collada_surfaces  
splist = surfaces_from_nodes(c.scene.nodes, color, Place(), {}, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 59, in surfaces_from_nodes  
spieces = surfaces_from_nodes(n.children, color, pl, instances, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 55, in surfaces_from_nodes  
instances[g.id] = spieces = geometry_node_surfaces(g.primitives, place, color,
materials, colors, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 97, in geometry_node_surfaces  
vcolors = vertex_colors(p, t, len(v), colors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/colorSites/D008-S1.ply

Unrecognized file suffix '.ply'  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/colorSites/D008.dae

Traceback (most recent call last):  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/__init__.py", line 129, in open  
return collada.read_collada_surfaces(session, data, file_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 21, in read_collada_surfaces  
splist = surfaces_from_nodes(c.scene.nodes, color, Place(), {}, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 59, in surfaces_from_nodes  
spieces = surfaces_from_nodes(n.children, color, pl, instances, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 55, in surfaces_from_nodes  
instances[g.id] = spieces = geometry_node_surfaces(g.primitives, place, color,
materials, colors, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 97, in geometry_node_surfaces  
vcolors = vertex_colors(p, t, len(v), colors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/ChimeraTest/sphere.dae.off.x3d

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/ChimeraTest/wood-meshlab.dae

Traceback (most recent call last):  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/__init__.py", line 129, in open  
return collada.read_collada_surfaces(session, data, file_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 21, in read_collada_surfaces  
splist = surfaces_from_nodes(c.scene.nodes, color, Place(), {}, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 59, in surfaces_from_nodes  
spieces = surfaces_from_nodes(n.children, color, pl, instances, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 55, in surfaces_from_nodes  
instances[g.id] = spieces = geometry_node_surfaces(g.primitives, place, color,
materials, colors, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 98, in geometry_node_surfaces  
c = material_color(materials.get(p.material), color)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 131, in material_color  
c8bit = tuple(int(255*r) for r in c)  
^^^^^^^^^^^^^^^^^^^^^^^  
TypeError: 'Map' object is not iterable  
  
TypeError: 'Map' object is not iterable  
  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 131, in material_color  
c8bit = tuple(int(255*r) for r in c)  
^^^^^^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/ChimeraTest/cube.dae

Traceback (most recent call last):  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/__init__.py", line 129, in open  
return collada.read_collada_surfaces(session, data, file_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 21, in read_collada_surfaces  
splist = surfaces_from_nodes(c.scene.nodes, color, Place(), {}, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 59, in surfaces_from_nodes  
spieces = surfaces_from_nodes(n.children, color, pl, instances, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 55, in surfaces_from_nodes  
instances[g.id] = spieces = geometry_node_surfaces(g.primitives, place, color,
materials, colors, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 83, in geometry_node_surfaces  
t = t.copy() # array from pycollada is not contiguous.  
^^^^^^  
AttributeError: 'NoneType' object has no attribute 'copy'  
  
AttributeError: 'NoneType' object has no attribute 'copy'  
  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 83, in geometry_node_surfaces  
t = t.copy() # array from pycollada is not contiguous.  
^^^^^^  
  
See log for complete Python traceback.  
  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/ChimeraTest/sphere.dae

Opened collada file sphere.dae  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/colorSites/test.dae

Traceback (most recent call last):  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/__init__.py", line 129, in open  
return collada.read_collada_surfaces(session, data, file_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 21, in read_collada_surfaces  
splist = surfaces_from_nodes(c.scene.nodes, color, Place(), {}, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 59, in surfaces_from_nodes  
spieces = surfaces_from_nodes(n.children, color, pl, instances, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 55, in surfaces_from_nodes  
instances[g.id] = spieces = geometry_node_surfaces(g.primitives, place, color,
materials, colors, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 97, in geometry_node_surfaces  
vcolors = vertex_colors(p, t, len(v), colors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/colorSites/test.dae

Traceback (most recent call last):  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/__init__.py", line 129, in open  
return collada.read_collada_surfaces(session, data, file_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 21, in read_collada_surfaces  
splist = surfaces_from_nodes(c.scene.nodes, color, Place(), {}, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 59, in surfaces_from_nodes  
spieces = surfaces_from_nodes(n.children, color, pl, instances, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 55, in surfaces_from_nodes  
instances[g.id] = spieces = geometry_node_surfaces(g.primitives, place, color,
materials, colors, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 97, in geometry_node_surfaces  
vcolors = vertex_colors(p, t, len(v), colors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> close session

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/colorSites/D008.dae

Traceback (most recent call last):  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 162, in _qt_safe  
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 119, in cmd_open  
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 195, in provider_open  
models, status = collated_open(session, None, [data], data_format,
_add_models,  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 483, in collated_open  
return remember_data_format()  
^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 454, in remember_data_format  
models, status = func(*func_args, **func_kw)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/__init__.py", line 129, in open  
return collada.read_collada_surfaces(session, data, file_name)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 21, in read_collada_surfaces  
splist = surfaces_from_nodes(c.scene.nodes, color, Place(), {}, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 59, in surfaces_from_nodes  
spieces = surfaces_from_nodes(n.children, color, pl, instances, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 55, in surfaces_from_nodes  
instances[g.id] = spieces = geometry_node_surfaces(g.primitives, place, color,
materials, colors, session)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 97, in geometry_node_surfaces  
vcolors = vertex_colors(p, t, len(v), colors)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
ValueError: shape mismatch: value array of shape (305322,3) could not be
broadcast to indexing result of shape (305322,4)  
  
File
"/Users/dchen/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/surface/collada.py", line 146, in vertex_colors  
vc[tarray.ravel(),:] = (colors[tc.ravel(),:]*255).astype(uint8)  
~~^^^^^^^^^^^^^^^^^^  
  
See log for complete Python traceback.  
  

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/colorSites/D008.dae

Opened collada file D008.dae  

> close session

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Data/AFRRI/colorSites/D008.dae

Opened collada file D008.dae  

> close session

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Public/AFRRI/DICOM format dicom

Summary of feedback from opening /Users/dchen/Library/CloudStorage/OneDrive-
NationalInstitutesofHealth/Public/AFRRI/DICOM  
---  
note | Opened 4 CT () as #1.1.1, grid size 512,512,178, pixel
0.545,0.545,2.98, shown at step 1, values float32  
  

> volume #1.1.1 region 0,0,0,511,511,177 step 2

[Repeated 1 time(s)]

> volume appearance brain

> volume appearance chest

> open /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Public/AFRRI/D030.dae

Opened collada file D030.dae  

> save /Users/dchen/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Public/AFRRI/minipig-dicom.cxs

——— End of log from Fri Jul 28 09:59:59 2023 ———

opened ChimeraX session  

> hide #2 models

> show #2 models

> volume #1.1.1 region 0,0,0,511,511,177 step 2

[Repeated 1 time(s)]

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #2 models

> show #2 models

> hide #!1 models

> hide #2 models

> show #2 models

> show #!1 models

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/D030.dae

Opened collada file D030.dae  

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/D008.dae

Opened collada file D008.dae  

> hide #2 models

> hide #3 models

> show #3 models

> show #2 models

> open /Users/cruzp2/Desktop/next_minipig.py

executed next_minipig.py  

> hide #2 models

> hide #3 models

> next

> show #3

> next

> hide #3

> show #2

> next

[Repeated 3 time(s)]

> hide #2

> open /Users/cruzp2/Desktop/next_minipig.py

FYI: command is replacing existing command: "next"  
executed next_minipig.py  

> next

> show #3

> hide #2

[Repeated 1 time(s)]

> next

> hide #3

> show #2

> next

> hide #2

> next

[Repeated 1 time(s)]

> show #3

> next

> hide #3

> show #2

> next

> hide #2

> vr button grip hand left command next

> save "/Users/cruzp2/Desktop/minipig_test_what_is saved.cxs"

——— End of log from Fri Jul 28 11:52:39 2023 ———

opened ChimeraX session  

> close #2

> close #3

> volume #1.1.1 region 0,0,0,511,511,177 step 2

[Repeated 1 time(s)]

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/D030.dae

Opened collada file D030.dae  

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/D008.dae

Opened collada file D008.dae  

> help help:user

> combine #3 close true modelID 2

Expected a keyword  

> combine #3 close true modelID #2

Expected a keyword  

> combine #3 close true modelID 2

Expected a keyword  

> combine #3 close true modelID 2

Expected a keyword  

> combine #3 close true modelID 2

Expected a keyword  

> combine #3 close true modelID 2 name D030.dae

Expected a keyword  

> combine 3 close true modelID 2 name D030.dae

Expected a keyword  

> combine #3 modelID 2 name D030.dae

Expected a keyword  

> combine #3 modelID #2 name D030.dae

Expected a keyword  

> combine #3 name D030.dae

No structures specified  

> close #3

> close #4

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/D030.dae

Opened collada file D030.dae  

> combine #3 name D030.dae

No structures specified  

> open /Users/cruzp2/Desktop/next_minipig.py

FYI: command is replacing existing command: "next"  
executed next_minipig.py  

> hide #!1.1 models

> hide #3 models

> next

> show #3

> show #!1.1 models

> hide #3 models

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/D008.dae

Opened collada file D008.dae  

> hide #4 models

> next

> hide #3

> show #4

> combine #3 name D030.dae

No structures specified  

> next

> hide #4

> next

[Repeated 1 time(s)]

> show #3

> next

> hide #3

> show #4

> next

> hide #4

> next

[Repeated 1 time(s)]

> show #3

> save /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/minipig-dicom_2.cxs

——— End of log from Fri Jul 28 14:14:40 2023 ———

opened ChimeraX session  

> hide #3 models

> show #3 models

> show #4 models

> hide #3 models

> hide #4 models

> close #3-4

> save "/Users/cruzp2/Desktop/minipig_test_what_is saved2.cxs"

——— End of log from Fri Jul 28 14:39:37 2023 ———

opened ChimeraX session  

> volume #1.1.1 region 0,0,0,511,511,177 step 2

[Repeated 1 time(s)]

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/D008.dae

Opened collada file D008.dae  

> open /Users/cruzp2/Library/CloudStorage/OneDrive-
> NationalInstitutesofHealth/Downloads/D030.dae

Opened collada file D030.dae  

> hide #2 models

> show #2 models

> hide #2 models

> hide #3 models

> open /Users/cruzp2/Desktop/next_minipig.py

executed next_minipig.py  

> next

> show #2

> next

> hide #2

> show #3

> next

> hide #3

> next

[Repeated 1 time(s)]

> show #2

> save "/Users/cruzp2/Desktop/minipig_test_what_is saved3.cxs"

——— End of log from Fri Jul 28 14:44:05 2023 ———

opened ChimeraX session  

Failed to send bug report. Bug report server www.rbvi.ucsf.edu is unavailable  

[Repeated 5 time(s)]




OpenGL version: 4.1 Metal - 76.3
OpenGL renderer: Apple M1 Max
OpenGL vendor: Apple

Python: 3.11.2
Locale: UTF-8
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: cocoa
Hardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,2
      Chip: Apple M1 Max
      Total Number of Cores: 10 (8 performance and 2 efficiency)
      Memory: 32 GB
      System Firmware Version: 8422.121.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.6.7 (21G651)
      Kernel Version: Darwin 21.6.0
      Time since boot: 3 days 16:59

Graphics/Displays:

    Apple M1 Max:

      Chipset Model: Apple M1 Max
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 24
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Thunderbolt Display:
          Resolution: 2560 x 1440 (QHD/WQHD - Wide Quad High Definition)
          UI Looks like: 2560 x 1440 @ 60.00Hz
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Rotation: Supported
          Automatically Adjust Brightness: Yes
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3456 x 2234 Retina
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal
        BenQ GW2750H:
          Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
          UI Looks like: 1920 x 1080 @ 60.00Hz
          Mirror: Off
          Online: Yes
          Rotation: Supported


Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2022.12.7
    cftime: 1.6.2
    charset-normalizer: 3.2.0
    ChimeraX-AddCharge: 1.5.11
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.46.1
    ChimeraX-AtomicLibrary: 10.0.8
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.4
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3.1
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.3
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7.dev202307280011
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.2
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.1
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2
    ChimeraX-Log: 1.1.5
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.2
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.1
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.9
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.2
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 3.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.1
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.9
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.1
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.1
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.31.1
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.1
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.1.3
    contourpy: 1.1.0
    cxservices: 1.2.2
    cycler: 0.11.0
    Cython: 0.29.33
    debugpy: 1.6.7
    decorator: 5.1.1
    docutils: 0.19
    executing: 1.2.0
    filelock: 3.9.0
    fonttools: 4.41.1
    funcparserlib: 1.0.1
    grako: 3.16.5
    h5py: 3.9.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.38
    imagecodecs: 2023.7.10
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.7
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.3.1
    jupyterlab-widgets: 3.0.8
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.7
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 21.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 10.0.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.9.1
    prompt-toolkit: 3.0.39
    psutil: 5.9.5
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3
    pyzmq: 25.1.0
    qtconsole: 5.4.3
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.4.1
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.4
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.1
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.2
    traitlets: 5.9.0
    typing-extensions: 4.7.1
    tzdata: 2023.3
    urllib3: 2.0.4
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.8

Change History (2)

comment:1 by Eric Pettersen, 2 years ago

Cc: Zach Pearson added
Component: Unassigned → Sessions
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → Collada not saved in session

comment:2 by Tom Goddard, 2 years ago

Resolution: → fixed
Status: assigned → closed

Fixed.

The Collada surfaces were not being saved in session files. When generic surfaces are read a line of code needs to be added (surface.SESSION_SAVE_DRAWING = True) has to be added to have the triangles saved in the session. The reason this is not the default behavior is that other surface code that defines its own session saving generally does not want the triangles saved.

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