ArtiaX: session save: Unknown class name 'Tomogram'

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Windows-10-10.0.22000
ChimeraX Version: 1.6.1 (2023-05-09 17:57:07 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.6.1 (2023-05-09)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> D:\xinglab\paper\data\segmentation\230213_12_005\230213_PDC_12_ts_005seg.mrc
> format mrc

Opened 230213_PDC_12_ts_005seg.mrc as #1, grid size 512,512,150, pixel
12,12,12, shown at level 0.00021, step 2, values float32  

> artiax start

Using preset: ArtiaX / Artiax Default  
Preset expands to these ChimeraX commands:

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> artiax add tomo #1

Opened 230213_PDC_12_ts_005seg.mrc as #2.1.1, grid size 512,512,150, pixel
12,12,12, shown at level 0.000214, step 1, values float32  

> artiax tomo #2.1.1 sliceDirection 0,0,1

> artiax view xy

> volume #2.1.1 style surface

> ui tool show "Segment Map"

Segmenting 230213_PDC_12_ts_005seg.mrc, density threshold 0.000214  
Showing 56 region surfaces  
1069 watershed regions, grouped to 56 regions  
Showing 230213_PDC_12_ts_005seg.seg - 56 regions, 56 surfaces  
Drag select of 2.1.1 230213_PDC_12_ts_005seg.mrc , 1580, 1572, 1575, 1554,
1585, 1544, 1581, 1519, 1578, 1584, 1582, 1579, 1541, 1505, 1586, 1576, 1489,
1556, 1587, 1573, 1534, 1500, 1565, 1577, 1588, 1583, 1540, 1571, 1552, 1562,
1539, 1447, 1502, 1536, 1564, 1568, 1563, 1491, 1559, 1119, 1480, 1462, 1411,
1263, 1196, 1466, 1345, 1395, 1070, 1547, 1387, 1479, 1524, 1163, 1526, 1551  

> ui tool show "Color Actions"

> color sel burly wood

> select ~sel

6 models selected  

> open
> D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_E1LDL_bin1_1200.star
> D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_E1LDR_bin1_1200.star
> D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_E1only_bin1_1200.star
> D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_E3_bin1_1200.star
> D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_PDCcore.star
> format star

Summary of feedback from opening
D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_E1LDL_bin1_1200.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_E1LDR_bin1_1200.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_E1only_bin1_1200.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_E3_bin1_1200.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Summary of feedback from opening
D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_PDCcore.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list 230213_PDC_12_ts_005_E1LDL_bin1_1200.star with 122
particles.  
Opened Particle list 230213_PDC_12_ts_005_E1LDR_bin1_1200.star with 143
particles.  
Opened Particle list 230213_PDC_12_ts_005_E1only_bin1_1200.star with 63
particles.  
Opened Particle list 230213_PDC_12_ts_005_E3_bin1_1200.star with 55 particles.  
Opened Particle list 230213_PDC_12_ts_005_PDCcore.star with 14 particles.  

> open
> D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_ATP_bin1_1200.star
> format star

Summary of feedback from opening
D:/xinglab/paper/data/segmentation/230213_12_005/230213_PDC_12_ts_005_ATP_bin1_1200.star  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list 230213_PDC_12_ts_005_ATP_bin1_1200.star with 632
particles.  
set axis size 22.5  
22.5  
['.arrow', '0', '0', '0', '22.5', '0', '0', '1.5', '6.0']  

> artiax particles #2.2.6 originScaleFactor 1.5

> artiax view xy

> artiax particles #2.2.6 color 0,46,86,100

> artiax particles #2.2.6 color 100,100,100,100

[Repeated 1 time(s)]

> artiax particles #2.2.6 color 10,100,100,100

> artiax particles #2.2.6 color 1,100,100,100

> artiax particles #2.2.6 color 8,100,100,100

> artiax particles #2.2.6 color 85,100,100,100

> artiax particles #2.2.6 color 85,10,100,100

> artiax particles #2.2.6 color 85,1,100,100

> artiax particles #2.2.6 color 85,9,100,100

> artiax particles #2.2.6 color 85,92,100,100

> artiax particles #2.2.6 color 85,92,10,100

> artiax particles #2.2.6 color 85,92,92,100

> open D:/xinglab/paper/data/segmentation/230213_12_005/ATP.mrc

Opened ATP.mrc as #3, grid size 60,60,60, pixel 6, shown at level 0.0712, step
1, values float32  

> artiax attach #3 toParticleList #2.2.6

Opened ATP.mrc as #2.2.6.1.1, grid size 60,60,60, pixel 6, shown at level
0.0712, step 1, values float32  

> volume #2.2.6.1.1 capFaces false

> artiax show #2.2.6 surfaces

Drag select of axes, 9 of 632 instances, surfaces, 9 of 632 instances, 9 atoms  
[Repeated 1 time(s)]fine  
Drag select of axes, 3 of 623 instances, surfaces, 2 of 623 instances, 2 atoms  
Drag select of axes, 2 of 623 instances, 2 atoms  
fine  
Drag select of axes, 3 of 620 instances, surfaces, 3 of 620 instances, 3 atoms  
Drag select of axes, 6 of 620 instances, surfaces, 6 of 620 instances, 6 atoms  
fine  
Drag select of axes, 1 of 614 instances, surfaces, 1 of 614 instances, 1 atoms  
[Repeated 1 time(s)]fine  
set axis size 22.5  
22.5  
['.arrow', '0', '0', '0', '22.5', '0', '0', '1.5', '6.0']  

> artiax particles #2.2.5 originScaleFactor 1.5

> artiax view xy

> artiax particles #2.2.5 color 17,81,28,100

> open D:/xinglab/paper/data/paper PDB/PDCcore_4.3A.mrc

Opened PDCcore_4.3A.mrc as #3, grid size 240,240,240, pixel 1.5, shown at
level 0.152, step 1, values float32  

> artiax attach #3 toParticleList #2.2.5

Opened PDCcore_4.3A.mrc as #2.2.5.1.1, grid size 240,240,240, pixel 1.5, shown
at level 0.152, step 1, values float32  

> volume #2.2.5.1.1 capFaces false

> artiax show #2.2.5 surfaces

set axis size 22.5  
22.5  
['.arrow', '0', '0', '0', '22.5', '0', '0', '1.5', '6.0']  

> artiax particles #2.2.4 originScaleFactor 1.5

> artiax view xy

> artiax particles #2.2.4 color 0,46,86,100

> open C:/Users/11574/Desktop/E3-15A.mrc

Opened E3-15A.mrc as #3, grid size 80,80,80, pixel 3, shown at level 0.0519,
step 1, values float32  

> artiax attach #3 toParticleList #2.2.4

Opened E3-15A.mrc as #2.2.4.1.1, grid size 80,80,80, pixel 3, shown at level
0.0519, step 1, values float32  

> volume #2.2.4.1.1 capFaces false

> artiax show #2.2.4 surfaces

> artiax particles #2.2.3 color 94,64,100,100

> artiax particles #2.2.3 color 88,45,40,100

> open C:/Users/11574/Desktop/E1-10.8A.mrc

Opened E1-10.8A.mrc as #3, grid size 80,80,80, pixel 3, shown at level 0.0924,
step 1, values float32  

> artiax attach #3 toParticleList #2.2.3

Opened E1-10.8A.mrc as #2.2.3.1.1, grid size 80,80,80, pixel 3, shown at level
0.0924, step 1, values float32  

> volume #2.2.3.1.1 capFaces false

> artiax show #2.2.3 surfaces

set axis size 22.5  
22.5  
['.arrow', '0', '0', '0', '22.5', '0', '0', '1.5', '6.0']  

> artiax particles #2.2.3 originScaleFactor 1.5

> artiax view xy

set axis size 22.5  
22.5  
['.arrow', '0', '0', '0', '22.5', '0', '0', '1.5', '6.0']  

> artiax particles #2.2.2 originScaleFactor 1.5

> artiax view xy

> artiax particles #2.2.2 color 94,64,100,100

> artiax particles #2.2.2 color 88,45,40,100

> open C:/Users/11574/Desktop/E1_LDR-7.5A.mrc

Opened E1_LDR-7.5A.mrc as #3, grid size 80,80,80, pixel 3, shown at level
0.11, step 1, values float32  

> artiax attach #3 toParticleList #2.2.2

Opened E1_LDR-7.5A.mrc as #2.2.2.1.1, grid size 80,80,80, pixel 3, shown at
level 0.11, step 1, values float32  

> volume #2.2.2.1.1 capFaces false

> artiax show #2.2.2 surfaces

set axis size 22.5  
22.5  
['.arrow', '0', '0', '0', '22.5', '0', '0', '1.5', '6.0']  

> artiax particles #2.2.1 originScaleFactor 1.5

> artiax view xy

> artiax particles #2.2.1 color 94,64,100,100

> artiax particles #2.2.1 color 88,45,40,100

set axis size 14.99991  
14.99991  
['.arrow', '0', '0', '0', '14.99991', '0', '0', '0.9999939999999999',
'3.9999759999999998']  
set axis size 14.99988  
14.99988  
['.arrow', '0', '0', '0', '14.99988', '0', '0', '0.999992', '3.999968']  
set axis size 14.99985  
14.99985  
['.arrow', '0', '0', '0', '14.99985', '0', '0', '0.99999', '3.99996']  

> open C:/Users/11574/Desktop/E1_LDL-8.3A.mrc

Opened E1_LDL-8.3A.mrc as #3, grid size 80,80,80, pixel 3, shown at level
0.101, step 1, values float32  

> artiax attach #3 toParticleList #2.2.1

Opened E1_LDL-8.3A.mrc as #2.2.1.1.1, grid size 80,80,80, pixel 3, shown at
level 0.101, step 1, values float32  

> volume #2.2.1.1.1 capFaces false

> artiax show #2.2.1 surfaces

> set bgColor gray

> save "D:/xinglab/paper/data/paper PDB/mito.cxs" includeMaps true

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 299, in process  
return copy_state(data, convert=convert)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 219, in copy_state  
return _copy(data)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
return convert(data)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 298, in convert  
return add_obj(obj, parents)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 476, in get_class  
return f(class_name)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'Tomogram'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002698F81AC40> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x00000269A6E77F70> 'segment map': Unknown class name 'Tomogram'  
  
ValueError: error processing: 'tools' -> -> 'segment map': Unknown class name
'Tomogram'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 299, in process  
return copy_state(data, convert=convert)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 219, in copy_state  
return _copy(data)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
return convert(data)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 298, in convert  
return add_obj(obj, parents)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 476, in get_class  
return f(class_name)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'Tomogram'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002698F81AC40> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x00000269A6E77F70> 'segment map': Unknown class name 'Tomogram'  
  
ValueError: error processing: 'tools' -> -> 'segment map': Unknown class name
'Tomogram'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Smoothing and grouping, standard deviation 9 voxels  
Showing 44 region surfaces  
Got 44 regions after smoothing 9 voxels.  
Drag select of 2.1.1 230213_PDC_12_ts_005seg.mrc , axes, 106 of 122 instances,
surfaces, 106 of 122 instances, axes, 123 of 143 instances, surfaces, 123 of
143 instances, axes, 58 of 63 instances, surfaces, 58 of 63 instances, axes,
42 of 55 instances, surfaces, 42 of 55 instances, axes, 12 of 14 instances,
surfaces, 12 of 14 instances, axes, 567 of 613 instances, surfaces, 566 of 613
instances, 1580, 27840 of 63620 triangles, 1575, 21297 of 40240 triangles,
1554, 19132 of 36624 triangles, 1585, 6234 of 32876 triangles, 1544, 878 of
23668 triangles, 1578, 1584, 1579, 1541, 15153 of 17464 triangles, 1505, 1576,
8428 of 16972 triangles, 1489, 1587, 1573, 1565, 1577, 5603 of 11856
triangles, 1588, 1571, 1973 of 10052 triangles, 1562, 1539, 1502, 1536, 1564,
22 of 11044 triangles, 1563, 1559, 1119, 1411, 1466, 1345, 1070, 3908 of 4956
triangles, 1387, 1524, 1163, 1591, 1593, 29926 of 40500 triangles, 1589, 32042
of 33920 triangles, 1592, 1594, 1590, 904 atoms  

> hide #!2.2.1 models

> hide #!2.2.2 models

> hide #!2.2.3 models

> hide #!2.2.4 models

> hide #!2.2.5 models

> hide #!2.2.6 models

> ui tool show "Color Actions"

> color sel burly wood

> select clear

> show #!2.2.1 models

> show #!2.2.2 models

> show #!2.2.3 models

> show #!2.2.4 models

> show #!2.2.5 models

> show #!2.2.6 models

> save "D:/xinglab/paper/data/paper PDB/whole.cxs" includeMaps true

Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 299, in process  
return copy_state(data, convert=convert)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 219, in copy_state  
return _copy(data)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
return convert(data)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 298, in convert  
return add_obj(obj, parents)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 476, in get_class  
return f(class_name)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'Tomogram'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002698F81AC40> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x00000269A6E77F70> 'segment map': Unknown class name 'Tomogram'  
  
ValueError: error processing: 'tools' -> -> 'segment map': Unknown class name
'Tomogram'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 299, in process  
return copy_state(data, convert=convert)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 219, in copy_state  
return _copy(data)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\state.py",
line 217, in _copy  
return convert(data)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 298, in convert  
return add_obj(obj, parents)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\toolshed\info.py", line 476, in get_class  
return f(class_name)  
File "C:\Users\11574\AppData\Local\UCSF\ChimeraX\1.6\site-
packages\chimerax\artiax\\__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'Tomogram'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 116, in <lambda>  
lambda *args, ses=session: show_save_file_dialog(ses), tool_tip="Save output
file",  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\dialog.py", line 51, in display  
run(session, cmd)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core\commands\cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\save_command\cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-
packages\chimerax\core_formats\\__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 625, in save  
mgr.discovery(self._state_containers)  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'tools' -> <chimerax.core.tools.Tools object at
0x000002698F81AC40> ->
<chimerax.segger.segment_dialog.VolumeSegmentationDialog object at
0x00000269A6E77F70> 'segment map': Unknown class name 'Tomogram'  
  
ValueError: error processing: 'tools' -> -> 'segment map': Unknown class name
'Tomogram'  
  
File "D:\ChimeraX1.6\ChimeraX\bin\lib\site-packages\chimerax\core\session.py",
line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
  
See log for complete Python traceback.  
  




OpenGL version: 3.3.0 - Build 27.20.100.8729
OpenGL renderer: Intel(R) UHD Graphics
OpenGL vendor: Intel

Python: 3.9.11
Locale: zh_CN.cp936
Qt version: PyQt6 6.4.2, Qt 6.4.2
Qt runtime version: 6.4.3
Qt platform: windows

Manufacturer: LENOVO
Model: 81TC
OS: Microsoft Windows 11 家庭中文版 (Build 22000)
Memory: 16,966,471,680
MaxProcessMemory: 137,438,953,344
CPU: 12 Intel(R) Core(TM) i7-10710U CPU @ 1.10GHz
OSLanguage: zh-CN

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.2.1
    Babel: 2.12.1
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    build: 0.10.0
    certifi: 2023.5.7
    cftime: 1.6.2
    charset-normalizer: 3.1.0
    ChimeraX-AddCharge: 1.5.9.1
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.3.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.9.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.43.10
    ChimeraX-AtomicLibrary: 10.0.6
    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: 2.0.1
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.8
    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: 1.6.1
    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: 1.1.1
    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: 1.1.1
    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-Label: 1.1.7
    ChimeraX-ListInfo: 1.1.1
    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: 2.0.12
    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: 1.3.7
    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: 1.0
    ChimeraX-NRRD: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.10.1
    ChimeraX-PDB: 2.7.2
    ChimeraX-PDBBio: 1.0
    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: 1.1
    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: 2.8.3
    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
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.10.3
    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: 2.2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Topography: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.28.4
    ChimeraX-uniprot: 2.2.2
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.2
    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
    comtypes: 1.1.14
    contourpy: 1.0.7
    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: 4.39.3
    funcparserlib: 1.0.1
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.8.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.35
    imagecodecs: 2022.9.26
    imagesize: 1.4.1
    importlib-metadata: 6.6.0
    ipykernel: 6.21.1
    ipython: 8.10.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.0.6
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.0.2
    jupyter-core: 5.3.0
    jupyterlab-widgets: 3.0.7
    kiwisolver: 1.4.4
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.2
    matplotlib: 3.6.3
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.2
    networkx: 2.8.8
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.4
    numpy: 1.23.5
    openvr: 1.23.701
    packaging: 23.1
    pandas: 2.0.3
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 9.3.0
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 3.5.0
    prompt-toolkit: 3.0.38
    psutil: 5.9.4
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.14.0
    pynrrd: 1.0.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.4.2
    PyQt6-Qt6: 6.4.3
    PyQt6-sip: 13.4.1
    PyQt6-WebEngine-commercial: 6.4.0
    PyQt6-WebEngine-Qt6: 6.4.3
    python-dateutil: 2.8.2
    pytz: 2023.3
    pywin32: 305
    pyzmq: 25.0.2
    qtconsole: 5.4.0
    QtPy: 2.3.1
    RandomWords: 0.4.0
    requests: 2.28.2
    scipy: 1.9.3
    setuptools: 67.4.0
    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
    starfile: 0.4.12
    superqt: 0.5.3
    tables: 3.7.0
    tcia-utils: 1.2.0
    tifffile: 2022.10.10
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.3.1
    traitlets: 5.9.0
    typing-extensions: 4.5.0
    tzdata: 2023.3
    urllib3: 1.26.15
    wcwidth: 0.2.6
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.7
    WMI: 1.5.1
    zipp: 3.15.0