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Opened 10 hours ago
#20421 new defect
ChimeraX bug report submission
| Reported by: | Owned by: | ||
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Unassigned | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | ||
| Project: |
Description
The following bug report has been submitted:
Platform: Linux-6.8.0-117-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.12rc202605142114 (2026-05-14 21:14:16 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
Startup Messages
---
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.
notes | CubeNTube: sphere eraser undo support enabled
/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/clipper/__init__.py:29: UserWarning: pkg_resources is
deprecated as an API. See
https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources
package is slated for removal as early as 2025-11-30. Refrain from using this
package or pin to Setuptools<81.
import pkg_resources
UCSF ChimeraX version: 1.12rc202605142114 (2026-05-14)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open run_class001.mrc
Opened run_class001.mrc as #1, grid size 72,72,72, pixel 3.82, shown at level
0.529, step 1, values float32
> artiax start
Using preset: ArtiaX / Artiax Default
Preset expands to these ChimeraX commands:
set bgColor black
lighting depthCue false
camera ortho
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin2/Refine3D/job002/run_data.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin2/Refine3D/job002/run_data.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 233, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 546, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 517, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin2/Refine3D/job002/run_data.star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin2/Refine3D/job002/run_data.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 233, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 546, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 517, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
Opened tomo186_7.65Apx.mrc as #2.1.1, grid size 1024,1024,400, pixel
7.65,7.65,7.65, shown at level 0.0272, step 1, values float32
> artiax clip off
> artiax tomo #2.1.1 sliceDirection 0,0,1
> artiax view xy
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin4/Refine3D/job005/run_data.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin4/Refine3D/job005/run_data.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 233, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 546, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 517, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
Array Excerpt (first 5 elements):
[-0.00287437 0.00365448 0.00344086 0.00590515 0.015625 ]
Basic Information:
Shape: (400, 1024, 1024)
Data type: float32
Size (number of elements): 419430400
Memory (bytes): 1677721600
Max value: 0.0784912109375
Min value: -0.1485595703125
Max value: 0.0784912109375
Min value: -0.1485595703125
Midpoint: -0.0350341796875
Inverted array (first 5 elements):
[-0.06719398 -0.07372284 -0.07350922 -0.07597351 -0.08569336]
Opened tomo186_7.65Apx_invert as #2.1.2, grid size 1024,1024,400, pixel
7.65,7.65,7.65, shown at level -0.0427, step 1, values float32
> artiax clip off
Array Excerpt (first 5 elements):
[-0.06719398 -0.07372284 -0.07350922 -0.07597351 -0.08569336]
Basic Information:
Shape: (400, 1024, 1024)
Data type: float32
Size (number of elements): 419430400
Memory (bytes): 1677721600
Max value: 0.0784912109375
Min value: -0.1485595703125
Max value: 0.0784912109375
Min value: -0.1485595703125
Midpoint: -0.0350341796875
Inverted array (first 5 elements):
[-0.00287437 0.00365448 0.00344086 0.00590515 0.015625 ]
Opened tomo186_7_invert as #2.1.3, grid size 1024,1024,400, pixel
7.65,7.65,7.65, shown at level 0.0272, step 1, values float32
> artiax clip off
[Repeated 1 time(s)]
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin4/Refine3D/job005/run_data.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin4/Refine3D/job005/run_data.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 233, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 546, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 517, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "add models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "remove models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
> artiax add tomo #1
Opened run_class001.mrc as #2.1.4, grid size 72,72,72, pixel 3.82, shown at
level 0.529, step 1, values float32
> artiax clip off
> artiax tomo #2.1.4 sliceDirection 0,0,1
> artiax view xy
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin2/Refine3D/job002/run_it000_data-new.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin2/Refine3D/job002/run_it000_data-new.star
---
notes | Processed as relion
Traceback (most recent call last):
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 233, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 546, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 517, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin2/Refine3D/job002/test_artiax_min.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin2/Refine3D/job002/test_artiax_min.star
---
notes | Processed as relion
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "model id changed":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "add models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
> artiax clip off
Opened Particle list test_artiax_min.star with 2 particles.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "add models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "remove models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin2/Refine3D/job002/test_artiax_min.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin2/Refine3D/job002/test_artiax_min.star
---
notes | Processed as relion
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "model id changed":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "add models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
> artiax clip off
Opened Particle list test_artiax_min.star with 2 particles.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "add models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "remove models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin4/Refine3D/job005/run_data.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin4/Refine3D/job005/run_data.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 233, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 546, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 517, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin4/Refine3D/job005/run_data.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin4/Refine3D/job005/run_data.star
---
notes | Processed as relion
Processed as relion
Traceback (most recent call last):
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/widgets/ArtiaxOpenDialog.py", line 66, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 138, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 233, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 546, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 517, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/formats.py", line 25, in open
return open_particle_list(session, data, file_name, format_name=self.name,
from_chimx=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/io.py", line 104, in open_particle_list
data = formats[format_name].particle_data(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 126, in
__init__
super().__init__(
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/ParticleData.py", line 507, in __init__
self.read_file()
File "/home/junhe/.local/share/ChimeraX/1.12/lib/python3.11/site-
packages/chimerax/artiax/io/RELION/RELIONParticleData.py", line 252, in
read_file
if np.issubdtype(df.dtypes[key], np.number):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
TypeError: Cannot interpret '<StringDtype(na_value=nan)>' as a data type
TypeError: Cannot interpret '' as a data type
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/numpy/core/numerictypes.py", line 417, in issubdtype
arg1 = dtype(arg1).type
^^^^^^^^^^^
See log for complete Python traceback.
> open /home/junhe/Desktop/warp-mt/relion-if-
> bin2/Refine3D/job002/test_artiax_min.star format star
Summary of feedback from opening /home/junhe/Desktop/warp-mt/relion-if-
bin2/Refine3D/job002/test_artiax_min.star
---
notes | Processed as relion
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "model id changed":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 464, in _items_change
self.set_value(next_val, delayed=True)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 404, in set_value
_when_all_updated(self, self.value_changed.emit)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
NameError: name 'self' is not defined
Error processing trigger "add models":
NameError: name 'self' is not defined
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/ui/widgets/item_chooser.py", line 534, in _when_all_updated
timer, old_func = self._wau_timer_info
^^^^
See log for complete Python traceback.
> artiax clip off
Opened Particle list test_artiax_min.star with 2 particles.
OpenGL version: 3.3.0 NVIDIA 580.159.03
OpenGL renderer: NVIDIA GeForce RTX 3080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.1
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Supermicro
Model: Super Server
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 192 AMD EPYC 7642 48-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 251Gi 20Gi 67Gi 9.9Gi 163Gi 218Gi
Swap: 2.0Gi 17Mi 2.0Gi
Graphics:
03:00.0 VGA compatible controller [0300]: ASPEED Technology, Inc. ASPEED Graphics Family [1a03:2000] (rev 52)
DeviceName: ASPEED Video AST2600
Subsystem: Super Micro Computer Inc ASPEED Graphics Family [15d9:1c22]
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.1
aiohttp: 3.13.1
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-doc: 0.0.4
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
autocommand: 2.2.2
babel: 2.18.0
backports.tarfile: 1.2.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.2.0
bs4: 0.0.2
build: 1.3.0
certifi: 2026.4.22
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-ArtiaX: 0.6.0
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Clipper: 0.23.0
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12rc202605142114
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-CubeNTube: 1.1.0
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.1
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: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.3.1
ChimeraX-locscalesurfer: 0.1.4
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
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-MatchAlign: 1.1
ChimeraX-MatchMaker: 2.4
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.8
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.6
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.0
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.0
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.20
decorator: 5.3.0
distro: 1.9.0
docutils: 0.21.2
einops: 0.8.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
fsspec: 2026.4.0
funcparserlib: 2.0.0a0
geomdl: 5.4.0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
hf-xet: 1.5.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
huggingface_hub: 1.15.0
idna: 3.15
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
importlib_metadata: 8.0.0
inflect: 7.3.1
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jaraco.collections: 5.1.0
jaraco.context: 5.3.0
jaraco.functools: 4.0.1
jaraco.text: 3.12.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
markdown-it-py: 4.2.0
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
mdurl: 0.1.2
more-itertools: 10.3.0
mpmath: 1.3.0
mrcfile: 1.5.4
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.21.2
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-cublas-cu12: 12.8.4.1
nvidia-cuda-cupti-cu12: 12.8.90
nvidia-cuda-nvrtc-cu12: 12.8.93
nvidia-cuda-runtime-cu12: 12.8.90
nvidia-cudnn-cu12: 9.10.2.21
nvidia-cufft-cu12: 11.3.3.83
nvidia-cufile-cu12: 1.13.1.3
nvidia-curand-cu12: 10.3.9.90
nvidia-cusolver-cu12: 11.7.3.90
nvidia-cusparse-cu12: 12.5.8.93
nvidia-cusparselt-cu12: 0.7.1
nvidia-nccl-cu12: 2.27.5
nvidia-nvjitlink-cu12: 12.8.93
nvidia-nvjitlink-cu12: 12.9.86
nvidia-nvshmem-cu12: 3.3.20
nvidia-nvtx-cu12: 12.8.90
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
packaging: 24.2
pandas: 3.0.3
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.9.6
platformdirs: 4.2.2
plotly: 6.7.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pyarrow: 24.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.17.1
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.10.2
PyQt6-Qt6: 6.10.1
PyQt6-WebEngine: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.1
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.28
PyYAML: 6.0.3
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
rich: 15.0.0
roman-numerals: 4.1.0
rpds-py: 0.30.0
safetensors: 0.7.0
scipy: 1.16.3
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
shellingham: 1.5.4
six: 1.17.0
snowballstemmer: 3.0.1
sortedcontainers: 2.4.0
soupsieve: 2.8.3
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.4
stack-data: 0.6.3
starfile: 0.5.13
starlette: 1.0.0
superqt: 0.7.6
sympy: 1.14.0
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
timm: 1.0.27
tinyarray: 1.2.5
tomli: 2.0.1
torch: 2.9.1
torchvision: 0.24.1
tornado: 6.5.5
tqdm: 4.67.3
traitlets: 5.14.3
triton: 3.5.1
typeguard: 4.3.0
typer: 0.25.1
typing-inspection: 0.4.2
typing_extensions: 4.15.0
typing_extensions: 4.12.2
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.47.0
wcwidth: 0.7.0
webcolors: 24.11.1
wheel: 0.45.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.23.0
zipp: 3.19.2
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