ArtiaX: arrays used as indices must be of integer (or boolean) type

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        macOS-12.5.1-arm64-arm-64bit
ChimeraX Version: 1.5 (2022-11-24 00:03:27 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.5 (2022-11-24)  
© 2016-2022 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_rec_flipped_corrected_labels_thylakoid.mrc

Opened Chlamy_ko_1h_004_rec_flipped_corrected_labels_thylakoid.mrc as #1, grid
size 698,960,200, pixel 13.1,13.1,13.1, shown at level 0.00225, step 2, values
int16  

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_rec_flipped_corrected_labels_chloroplast.mrc

Opened Chlamy_ko_1h_004_rec_flipped_corrected_labels_chloroplast.mrc as #2,
grid size 698,960,200, pixel 13.1,13.1,13.1, shown at level 0.0021, step 2,
values int16  

> volume #1 step 1

> volume #2 step 1

> ui tool show "Map Coordinates"

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\xd' for virtual key 36 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> artiax start

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

    
    
    set bgColor black
    lighting depthCue false
    camera ortho

  

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_1_bin6_70S.em
> format motl

Summary of feedback from opening
/Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_1_bin6_70S.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list Chlamy_ko_1h_004_1_bin6_70S.em with 204 particles.  
set axis size 196.2  
196.2  
['.arrow', '0', '0', '0', '196.2', '0', '0', '13.08', '52.32']  

> artiax particles #3.2.1 originScaleFactor 13.08

> artiax view xy

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_1_bin6_80S.em
> format motl

Summary of feedback from opening
/Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_1_bin6_80S.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list Chlamy_ko_1h_004_1_bin6_80S.em with 994 particles.  
set axis size 196.2  
196.2  
['.arrow', '0', '0', '0', '196.2', '0', '0', '13.08', '52.32']  

> artiax particles #3.2.2 originScaleFactor 13.08

> artiax view xy

> artiax hide axes

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/70S_PDB6W6P_20.mrc

Opened 70S_PDB6W6P_20.mrc as #4, grid size 60,58,51, pixel 6.67,6.67,6.67,
shown at level 0.31, step 1, values float32  

> artiax attach #4 toParticleList #3.2.1

Opened 70S_PDB6W6P_20.mrc as #3.2.1.1.1, grid size 60,58,51, pixel
6.67,6.67,6.67, shown at level 0.31, step 1, values float32  

> volume #3.2.1.1.1 capFaces false

> artiax show #3.2.1 surfaces

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/80S_PDB&MPI_20.mrc

Opened 80S_PDB&MPI_20.mrc as #4, grid size 53,56,62, pixel 6.67,6.67,6.67,
shown at level 0.344, step 1, values float32  

> artiax attach #4 toParticleList #3.2.2

Opened 80S_PDB&MPI_20.mrc as #3.2.2.1.1, grid size 53,56,62, pixel
6.67,6.67,6.67, shown at level 0.344, step 1, values float32  

> volume #3.2.2.1.1 capFaces false

> artiax show #3.2.2 surfaces

> artiax particles #3.2.2 surfaceLevel 0.2807

> volume #3.2.1.1.1 level 0.2292

> volume #3.2.1.1.1 level 0.256

> artiax hide markers

> artiax particles #3.2.2 surfaceLevel 0.11499

> artiax particles #3.2.1 surfaceLevel 0.1989

> artiax particles #3.2.1 surfaceLevel 0.05439

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1e' for virtual key 126 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> volume #1 surfaceSmoothing true

> volume #1 smoothingIterations 8

> volume #1 smoothingFactor 0.8

> volume #2 surfaceSmoothing true

> volume #2 smoothingFactor 0.8

[Repeated 2 time(s)]

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(NoModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ControlModifier|AltModifier|MetaModifier)  

Mismatch between Cocoa '\x0' and Carbon '\x1f' for virtual key 125 with
QFlags<Qt::KeyboardModifier>(ShiftModifier|ControlModifier|AltModifier|MetaModifier)  

> volume #2 smoothingIterations 8

> lighting soft

> lighting simple

Opened Chlamy_ko_1h_004_rec_flipped_corrected.mrc as #3.1.1, grid size
698,960,200, pixel 13.1,13.1,13.1, shown at level 0.124, step 1, values
float32  

> artiax tomo #3.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax tomo #3.1.1 slice 119

> artiax tomo #3.1.1 slice 85

> ui mousemode right select

> select #3.2.1.1.1

2 models selected  

> ui mousemode right "delete picked particle"

[Repeated 1 time(s)]

> artiax show markers

> volume #3.1.1 level -5.142,0 level -0.3707,0.5 level 1.225,1

> volume #3.1.1 level -5.142,0 level -0.01945,0.9 level 1.225,1

> volume #3.1.1 level -3.147,0 level -0.01945,0.9 level 1.225,1

> volume #3.1.1 region 0,0,98,697,959,98 step 1 showOutlineBox true imageMode
> "full region"

> volume #3.1.1 level -3.147,0 level 0.0641,0.8077 level 1.225,1

> artiax particles #3.2.1 color 37,95,95,100

> lighting soft

> hide #!3.1.1 models

> artiax particles #3.2.1 color 0,60,56,100

> artiax particles #3.2.1 color 37,95,95,100

> volume #1 color #b2e0b2

> volume #1 color #b2dab2

> volume #1 color #b2deb2

> volume #2 color #00ffb2

> volume #2 color lime

> volume #2 color #009d00

> volume #2 color #008e00

> set bgColor white

> set bgColor #ffffff00

> volume #2 color #009900

> set bgColor black

> set bgColor transparent

> volume #2 color #006e00

> volume #2 color #929292

> volume #2 color #ff40ff

> volume #2 color #ff2600

> volume #2 color #919191

> volume #2 color #009051

> volume #2 color #009193

> volume #2 color #009051

> artiax particles #3.2.1 color 37,95,95,100

> artiax particles #3.2.1 color 46,84,100,100

> artiax particles #3.2.1 color 48,51,100,100

> artiax particles #3.2.1 color 46,84,100,100

> artiax particles #3.2.1 color 0,59,100,100

> artiax particles #3.2.1 color 46,84,100,100

> artiax particles #3.2.1 color 2,20,100,100

> artiax particles #3.2.1 color 0,59,100,100

> artiax particles #3.2.2 color 0,46,86,100

> artiax particles #3.2.2 color 2,20,100,100

> artiax particles #3.2.2 color 0,59,100,100

> artiax particles #3.2.1 color 0,59,100,100

> artiax particles #3.2.1 color 46,84,100,100

> save /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/004.cxs

Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x1220b3ac0> ->
<chimerax.atomic.molobject.Atom object at 0x168e1a300> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x1220b3ac0> ->
<chimerax.atomic.molobject.Atom object at 0x168e1a300> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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.  
  

> ui tool show "Map Eraser"

> lighting simple

Can only have one displayed volume when erasing  

[Repeated 5 time(s)]

> volume #2 smoothingIterations 20

> volume #2 smoothingIterations 100

> volume #1 smoothingIterations 100

> volume #1 smoothingIterations 10

> volume #1 smoothingIterations 20

> volume #2 smoothingIterations 20

> volume #2 smoothingFactor 1

> volume #2 smoothingFactor 10

/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/bounds.py:53: RuntimeWarning: overflow encountered
in multiply  
r = 0.5*sqrt((size*size).sum())  
/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/camera.py:632: RuntimeWarning: invalid value
encountered in double_scalars  
e = 1 / (z_far - z_near)  
/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py:998: RuntimeWarning: invalid value
encountered in double_scalars  
return (n + (f-n)*lp.depth_cue_start,  
/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/graphics/opengl.py:999: RuntimeWarning: invalid value
encountered in double_scalars  
n + (f-n)*lp.depth_cue_end)  

> volume #2 smoothingFactor 1

> volume #2 smoothingFactor 1.5

> volume #2 smoothingFactor 1.2

> volume #2 smoothingFactor 0.3

> volume #2 smoothingFactor 0.2

> volume #2 smoothingIterations 100

> volume #1 smoothingFactor 0.2

> volume #1 smoothingIterations 100

> lighting soft

> show #!3.1.1 models

> artiax tomo #3.1.1 slice 1

> artiax tomo #3.1.1 slice 0

> lighting simple

> artiax tomo #3.1.1 slice 0

[Repeated 2 time(s)]

> hide #!3.1.1 models

> show #!3.1.1 models

> artiax tomo #3.1.1 slice 0

[Repeated 1 time(s)]

> artiax tomo #3.1.1 slice 1

> artiax tomo #3.1.1 slice 2

[Repeated 1 time(s)]

> artiax tomo #3.1.1 slice 1

> artiax tomo #3.1.1 slice 2

Opened Chlamy_ko_1h_004_rec_flipped_corrected.mrc as #3.1.1, grid size
698,960,200, pixel 13.1,13.1,13.1, shown at level 0.124, step 1, values
float32  

> artiax tomo #3.1.1 sliceDirection 0,0,1

> artiax view xy

> artiax tomo #3.1.1 slice 99

> artiax tomo #3.1.1 slice 94

> artiax tomo #3.1.1 slice 76

> artiax tomo #3.1.1 slice 74

> lighting soft

> hide #!3.1.1 models

> set bgColor white

> set bgColor #ffffff00

> view orient

[Repeated 1 time(s)]

> set bgColor black

> set bgColor transparent

> set bgColor gray

> set bgColor #80808000

> set bgColor white

> set bgColor #ffffff00

> set bgColor black

> set bgColor transparent

> save /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/004.cxs

Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x1220b3ac0> ->
<chimerax.atomic.molobject.Atom object at 0x168e1a300> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x1220b3ac0> ->
<chimerax.atomic.molobject.Atom object at 0x168e1a300> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 48, in display  
cmd += ' ' + save_mgr.save_args_string_from_widget(fmt, self._current_option)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/manager.py", line 110, in
save_args_string_from_widget  
return provider_info.bundle_info.run_provider(self.session,  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/io/formats.py", line 70, in
save_args_string_from_widget  
return widget.get_argument_string()  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/widgets/SaveArgsWidget.py", line 93, in
get_argument_string  
id_string = self.manager_model.get(mdl_idx).id_string  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/util/ManagerModel.py", line 54, in get  
return func(identifier)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/util/ManagerModel.py", line 198, in _get_by_idx  
return self.child_models()[idx]  
IndexError: list index out of range  
  
IndexError: list index out of range  
  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/util/ManagerModel.py", line 198, in _get_by_idx  
return self.child_models()[idx]  
  
See log for complete Python traceback.  
  

> save /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/004.cxs
> includeMaps true

Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x1220b3ac0> ->
<chimerax.atomic.molobject.Atom object at 0x168e1a300> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 262, in discovery  
self.processed[key] = self.process(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 299, in process  
return copy_state(data, convert=convert)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 219, in copy_state  
return _copy(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in _copy  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 204, in <listcomp>  
items = [(_copy(k), _copy(v)) for k, v in data.items()]  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/state.py", line 217, in _copy  
return convert(data)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 298, in convert  
return add_obj(obj, parents)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 270, in _add_obj  
uid = _UniqueName.from_obj(self.session, obj)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 142, in from_obj  
if obj_cls != bundle_info.get_class(obj_cls.__name__, session.logger):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 476, in get_class  
return f(class_name)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/__init__.py", line 37, in get_class  
raise ValueError("Unknown class name '%s'" % class_name)  
ValueError: Unknown class name 'MarkerSetPlus'  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 127, in show_save_file_dialog  
_dlg.display(session, **kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/dialog.py", line 51, in display  
run(session, cmd)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 38, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 75, in cmd_save  
Command(session, registry=registry).run(provider_cmd_text, log=log)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2897, in run  
result = ci.function(session, **kw_args)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/save_command/cmd.py", line 90, in provider_save  
saver_info.save(session, path, **provider_kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core_formats/__init__.py", line 84, in save  
return cxs_save(session, path, **kw)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 899, in save  
session.save(output, version=version, include_maps=include_maps)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 625, in save  
mgr.discovery(self._state_containers)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/session.py", line 266, in discovery  
raise ValueError("error processing: %s: %s" % (_obj_stack(parents, obj), e))  
ValueError: error processing: 'attribute registration' ->
<chimerax.core.attributes.RegAttrManager object at 0x1220b3ac0> ->
<chimerax.atomic.molobject.Atom object at 0x168e1a300> 'M': Unknown class name
'MarkerSetPlus'  
  
ValueError: error processing: 'attribute registration' -> -> 'M': Unknown
class name 'MarkerSetPlus'  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/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.  
  

> save /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/004.obj

> open /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/004.obj

Opened OBJ file 004.obj containing 6 objects, 28216324 triangles  

> hide #!3.2.1 models

> hide #!3.2.2 models

> show #!3.2.2 models

> hide #!3.2.2 models

> lighting simple

> ui mousemode right select

Drag select of ArtiaX Particle Lists Chlamy_ko_1h_004_1_bin6_80S.em Markers
atoms, 206418 of 1988000 triangles, ArtiaX Particle Lists
Chlamy_ko_1h_004_1_bin6_80S.em Particles surfaces, 2088172 of 20150368
triangles  

> select clear

> select #4.3

1 model selected  

> hide #4.6 models

> show #4.6 models

> hide #4.1 models

> show #4.1 models

> hide #4.2 models

> show #4.2 models

> hide #4.3 models

> show #4.3 models

> color #4.3 #00f900ff

> hide #4.3 models

> show #4.3 models

> select add #4

7 models selected  

> select subtract #4

Nothing selected  

> close #4

> show #!1 models

> show #!2 models

> show #!3.1.1 models

> show #!3.2.1 models

> hide #!3.1.1 models

> show #!3.2.2 models

> lighting soft

> volume #1 smoothingIterations 300

> volume #1 smoothingIterations 50

> volume #1 smoothingIterations 100

> volume #1 smoothingIterations 200

> volume #1 smoothingIterations 100

> select #3.2.2.2

1 model selected  

> select clear

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_1_bin6_ATPase.em
> format motl

Summary of feedback from opening
/Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_1_bin6_ATPase.em  
---  
notes | 15  
['.arrow', '0', '0', '0', '15', '0', '0', '1.0', '4.0']  
  
Opened Particle list Chlamy_ko_1h_004_1_bin6_ATPase.em with 193 particles.  
set axis size 196.2  
196.2  
['.arrow', '0', '0', '0', '196.2', '0', '0', '13.08', '52.32']  

> artiax particles #3.2.3 originScaleFactor 13.08

> artiax view xy

> lighting simple

> hide #!3.2.2 models

> show #!3.2.2 models

> hide #!3.2.3 models

> show #!3.2.3 models

> hide #!3.2.2 models

> hide #!3.2.1 models

Drag select of axes, 1 of 193 instances, 1 atoms  

> ui mousemode right "delete picked particle"

fine  

> ui mousemode right select

Drag select of axes, 2 of 192 instances, 1 atoms  
fine  

> artiax hide axes

Drag select of 1 atoms  
fine  
Drag select of 4 atoms  
fine  
Drag select of 3 atoms  
fine  
Drag select of 1 atoms  
fine  
Drag select of 5 atoms  
fine  
Drag select of 1 atoms  
fine  
Drag select of 4 atoms  
fine  
Drag select of 4 atoms  
fine  
Drag select of 2 atoms  
fine  
Drag select of 8 atoms  
fine  
Drag select of 2 atoms  
fine  
Drag select of 1 atoms  
fine  
Drag select of 1 atoms  
fine  
Drag select of 3 atoms  
fine  
Drag select of 1 atoms  
fine  
Drag select of 1 atoms  
fine  
Drag select of 1 atoms  
fine  
Drag select of 2 atoms  
fine  

> show #!3.1.1 models

> artiax tomo #3.1.1 slice 85

Drag select of 1 atoms  
fine  
Drag select of 2 atoms  
fine  
Drag select of 1 atoms  
fine  

> artiax tomo #3.1.1 slice 127

> hide #!3.2.3 models

> show #!3.2.3 models

> hide #!3.2.3 models

> artiax tomo #3.1.1 slice 126

> show #!3.2.3 models

> select #3.2.3.3/M:64@M

1 atom, 1 residue, 1 model selected  
fine  

> artiax tomo #3.1.1 slice 125

> select #3.2.3.3/M:48@M

1 atom, 1 residue, 1 model selected  
fine  

> artiax tomo #3.1.1 slice 144

> artiax tomo #3.1.1 slice 165

> select #3.2.3.3/M:23@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:27@M

1 atom, 1 residue, 1 model selected  
fine  

> hide #!3.2.3 models

> artiax tomo #3.1.1 slice 171

> show #!3.2.3 models

> artiax tomo #3.1.1 slice 156

> artiax tomo #3.1.1 slice 165

> select #3.2.3.3/M:35@M

1 atom, 1 residue, 1 model selected  
fine  

> select clear

> select #3.2.3.3/M:104@M

1 atom, 1 residue, 1 model selected  
fine  

> artiax tomo #3.1.1 slice 111

> artiax tomo #3.1.1 slice 112

> artiax tomo #3.1.1 slice 21

Drag select of 2 atoms  

> ui mousemode right "translate selected particles"

> artiax tomo #3.1.1 slice 105

> artiax tomo #3.1.1 slice 113

> ui mousemode right select

> select clear

> select #3.2.3.3/M:140@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:133@M

1 atom, 1 residue, 1 model selected  
Drag select of 1 Chlamy_ko_1h_004_rec_flipped_corrected_labels_thylakoid.mrc  

> select #3.2.3.3/M:133@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:144@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> view orient

> artiax tomo #3.1.1 slice 141

> artiax tomo #3.1.1 slice 83

> artiax tomo #3.1.1 slice 46

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/PDB7JG7_ATPsynthase_rescaled.mrc

Opened PDB7JG7_ATPsynthase_rescaled.mrc as #4, grid size 138,142,192, pixel
2.18,2.18,2.18, shown at level 0.123, step 1, values float32  

> artiax attach #4 toParticleList #3.2.3

Opened PDB7JG7_ATPsynthase_rescaled.mrc as #3.2.3.1.1, grid size 138,142,192,
pixel 2.18,2.18,2.18, shown at level 0.123, step 1, values float32  

> volume #3.2.3.1.1 capFaces false

> artiax show #3.2.3 surfaces

> ui mousemode right select

> select #3.2.3.3/M:12@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> hide #!3.1.1 models

> hide #!3.2.3 models

> open
> /Users/zhenhou/Desktop/manuscripts/2023/Nucleosome/movie_whole_tomo_py/lamellae_014_1_labels_cleaned.mrc

Opened lamellae_014_1_labels_cleaned.mrc as #4, grid size 630,662,270, pixel
13.1,13.1,13.1, shown at level 126, step 2, values int16  

> volume #4 level 124

> volume #4 step 1

> volume #14smoothingIteration 100

Expected a density maps specifier or a keyword  

> volume #4 surfaceSmoothing true

> close #4

> close #3.2.3.1.1

> close #3.1.1

> close #1

> close #2

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_rec_flipped_corrected_labels_chloroplast.mrc

Opened Chlamy_ko_1h_004_rec_flipped_corrected_labels_chloroplast.mrc as #1,
grid size 698,960,200, pixel 13.1,13.1,13.1, shown at level 6, step 2, values
int16  

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_rec_flipped_corrected_labels_thylakoid.mrc

Opened Chlamy_ko_1h_004_rec_flipped_corrected_labels_thylakoid.mrc as #2, grid
size 698,960,200, pixel 13.1,13.1,13.1, shown at level 0.00025, step 2, values
int16  

> volume #1 surfaceSmoothing true

> volume #1 smoothingIterations 100

> volume #1 smoothingIterations 50

> volume #1 smoothingFactor 0.2

> volume #1 smoothingIterations 10

> volume #1 smoothingIterations 40

> volume #1 smoothingIterations 50

> volume #2 surfaceSmoothing true

> volume #2 smoothingIterations 50

> volume #2 smoothingFactor 0.2

> volume #2 smoothingFactor 0.3

> artiax add tomo #2

Opened Chlamy_ko_1h_004_rec_flipped_corrected_labels_thylakoid.mrc as #3.1.1,
grid size 698,960,200, pixel 13.1,13.1,13.1, shown at level 0.00025, step 1,
values int16  

> artiax tomo #3.1.1 sliceDirection 0,0,1

> artiax view xy

> hide #!3.1.1 models

> show #!3.1.1 models

> hide #!3.1.1 models

> show #!3.1.1 models

> hide #!3.1.1 models

> show #!3.1.1 models

> hide #!3.1.1 models

> show #!3.1.1 models

> hide #!3.1.1 models

> show #!3.1.1 models

> hide #!3.1.1 models

> show #!3.1.1 models

> hide #!3.1.1 models

> volume #1 step 1

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_004_rec_flipped_corrected_labels_thylakoid.mrc

Opened Chlamy_ko_1h_004_rec_flipped_corrected_labels_thylakoid.mrc as #2, grid
size 698,960,200, pixel 13.1,13.1,13.1, shown at level 0.00025, step 2, values
int16  

> volume #2 step 1

> volume #2 surfaceSmoothing true

> volume #2 smoothingFactor 0.3

> volume #2 smoothingIterations 50

> volume #2 smoothingFactor 0.5

> volume #2 smoothingFactor 0.3

> volume #2 smoothingIterations 60

> volume #2 smoothingFactor 0.6

> volume #2 smoothingFactor 0.4

> volume #1 smoothingFactor 0.4

> volume #1 smoothingIterations 60

> lighting soft

> show #!3.2.2 models

> show #!3.2.3 models

> show #!3.2.1 models

> lighting simple

> volume #1 color #008f00

> volume #1 color #009051

> volume #2 color #00fa92

> volume #2 color #00ff92

> volume #2 color cyan

> volume #2 color #009193

> volume #2 color #4f8f00

> volume #2 color #d4fb79

> volume #2 color #73fa79

> volume #2 color #00f900

> volume #2 color #73fcd6

> volume #2 color #73fa79

> lighting soft

> volume #2 color #00f900

> volume #2 color lime

[Repeated 2 time(s)]

> volume #2 color #00ff8c

> volume #2 color #00ad8c

> volume #2 color #80ad8c

> volume #2 color #80f68c

> lighting simple

> hide #!3.2.1 models

> hide #!3.2.2 models

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:22@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.2

1 model selected  

> select #3.2.3.3/M:133@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:15@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:140@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:19@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.2

1 model selected  

> select clear

> select #3.2.3.3/M:24@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:6@M

1 atom, 1 residue, 1 model selected  

> select #3.2.3.3/M:21@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:32@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:17@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:2@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select clear

[Repeated 1 time(s)]

> select #3.2.3.3/M:25@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:13@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:5@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:3@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:33@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:144@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:9@M

1 atom, 1 residue, 1 model selected  

> select #3.2.3.3/M:18@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:36@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:28@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:20@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:141@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:11@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select clear

> select #3.2.3.3/M:1@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:26@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:31@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:16@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:8@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:7@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:0@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:14@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select clear

> select #3.2.3.3/M:120@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:84@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:14@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:0@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:106@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:125@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:151@M

1 atom, 1 residue, 1 model selected  
fine  

> select #1

2 models selected  

> select clear

> select #3.2.3.3/M:125@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.2

1 model selected  

> select #3.2.3.3/M:62@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:138@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:71@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:107@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:75@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:40@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select clear

> select #3.2.3.2

1 model selected  

> select #3.2.3.3/M:73@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:131@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:115@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

fine  

> ui mousemode right select

> select #3.2.3.3/M:49@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:97@M

1 atom, 1 residue, 1 model selected  

> select #3.2.3.3/M:97@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  
Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  

[lots of these deleted]

Traceback (most recent call last):  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 638, in <lambda>  
gw.mouseMoveEvent = lambda e, s=self: s._dispatch_mouse_event(e, "mouse_drag")  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/mouse_modes/mousemodes.py", line 537, in
_dispatch_mouse_event  
f(MouseEvent(event, modifiers=modifiers))  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 36, in mouse_drag  
self._rotate(axis, angle)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/mouse.py", line 72, in _rotate  
rotate_instances(saxis, angle, self._collections, self._masks)  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
rotate_instances  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 617, in
<listcomp>  
b = bounds.union_bounds([d.masked_bounds(m) for d, m in zip(drawings, masks)])  
File "/Users/zhenhou/Library/Application Support/ChimeraX/1.5/site-
packages/chimerax/artiax/particle/SurfaceCollectionModel.py", line 400, in
masked_bounds  
spos = self.child_positions.masked(mask)  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
IndexError: arrays used as indices must be of integer (or boolean) type  
  
File
"/Users/zhenhou/Desktop/ChimeraX-1.5.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/geometry/place.py", line 728, in masked  
p = Places(place_array=self.array()[mask])  
  
See log for complete Python traceback.  
  

> ui mousemode right select

> select #3.2.3.3/M:184@M

1 atom, 1 residue, 1 model selected  
fine  

> ui mousemode right select

> select #3.2.3.3/M:117@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:93@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:80@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:51@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:97@M

1 atom, 1 residue, 1 model selected  
fine  

> ui mousemode right select

> select #3.2.3.3/M:58@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:37@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:135@M

1 atom, 1 residue, 1 model selected  
fine  

> ui mousemode right select

> select #3.2.3.3/M:112@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:69@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:58@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:174@M

1 atom, 1 residue, 1 model selected  
fine  

> ui mousemode right select

Drag select of surfaces, 2 of 118 instances, 2 atoms  
fine  

> ui mousemode right select

> select #3.2.3.3/M:165@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:180@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:185@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:169@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:160@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:176@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:187@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select clear

> select #3.2.3.3/M:185@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:124@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

fine  

> ui mousemode right select

> select #3.2.3.3/M:109@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:45@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:74@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:99@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:42@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:43@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:132@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.2

1 model selected  

> select #3.2.3.3/M:94@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:94@M

1 atom, 1 residue, 1 model selected  

> select clear

> select #3.2.3.3/M:94@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:148@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:46@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:134@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select clear

[Repeated 1 time(s)]

> select #3.2.3.3/M:89@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:65@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:102@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:86@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

fine  

> ui mousemode right select

> select #3.2.3.3/M:52@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:146@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:52@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:105@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:30@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:70@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:60@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:66@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:149@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:85@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:142@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:152@M

1 atom, 1 residue, 1 model selected  
fine  

> ui mousemode right select

> select #3.2.3.3/M:83@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:90@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:100@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:98@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

fine  

> ui mousemode right select

> select #3.2.3.2

1 model selected  

> select #3.2.3.2

1 model selected  

> select #3.2.3.3/M:136@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:56@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:53@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:105@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:113@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:61@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:150@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:87@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:57@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.3/M:81@M

1 atom, 1 residue, 1 model selected  
fine  

> select #3.2.3.2

1 model selected  

> select #3.2.3.3/M:121@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:34@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:76@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:91@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:77@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:126@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> artiax hide markers

> hide #!3.2.3 models

> show #!3.2.3 models

> artiax particles #3.2.3 color 100,64,2,100

> artiax particles #3.2.3 color 100,80,60,100

> artiax hide markers

> open
> /Users/zhenhou/Desktop/Thylakoid_1h_seg/corrected_tomos/PDB7JG7_ATPsynthase_rescaled.mrc

Opened PDB7JG7_ATPsynthase_rescaled.mrc as #4, grid size 138,142,192, pixel
2.18,2.18,2.18, shown at level 0.123, step 1, values float32  

> artiax attach #4 toParticleList #3.2.3

Opened PDB7JG7_ATPsynthase_rescaled.mrc as #3.2.3.1.1, grid size 138,142,192,
pixel 2.18,2.18,2.18, shown at level 0.123, step 1, values float32  

> volume #3.2.3.1.1 capFaces false

> artiax show #3.2.3 surfaces

> artiax particles #3.2.3 surfaceLevel 0.04413

> artiax show markers

> ui mousemode right select

> select #3.2.3.3/M:87@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:127@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:134@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> artiax hide markers

> volume #2 color #80f687

> volume #2 color #aff687

> volume #2 color #baf687

> volume #1 color #00c851

> show #!3.2.2 models

> show #!3.2.1 models

> artiax particles #3.2.3 color 100,64,2,100

> lighting soft

> ui mousemode right select

> select clear

> set bgColor white

> set bgColor #ffffff00

> lighting simple

> view orient

[Repeated 1 time(s)]

> ui tool show "Side View"

> lighting soft

> artiax particles #3.2.1 color 0,46,86,100

> artiax particles #3.2.1 color 0,20,50,100

> artiax particles #3.2.1 color 37,95,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,94,95,100

> artiax particles #3.2.1 color 37,93,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,92,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,91,95,100

[Repeated 3 time(s)]

> artiax particles #3.2.1 color 37,90,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,89,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,88,95,100

> artiax particles #3.2.1 color 37,87,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,86,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,85,95,100

[Repeated 3 time(s)]

> artiax particles #3.2.1 color 37,84,95,100

[Repeated 3 time(s)]

> artiax particles #3.2.1 color 37,83,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,82,95,100

> artiax particles #3.2.1 color 37,81,95,100

[Repeated 3 time(s)]

> artiax particles #3.2.1 color 37,80,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,79,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,77,95,100

> artiax particles #3.2.1 color 37,75,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,73,95,100

> artiax particles #3.2.1 color 37,72,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,71,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,70,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,69,95,100

[Repeated 4 time(s)]

> artiax particles #3.2.1 color 37,68,95,100

> artiax particles #3.2.1 color 37,67,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,65,95,100

[Repeated 4 time(s)]

> artiax particles #3.2.1 color 37,66,95,100

> artiax particles #3.2.1 color 37,67,95,100

> artiax particles #3.2.1 color 37,68,95,100

> artiax particles #3.2.1 color 37,69,95,100

> artiax particles #3.2.1 color 37,71,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,72,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,73,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,74,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,75,95,100

[Repeated 3 time(s)]

> artiax particles #3.2.1 color 37,76,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,77,95,100

> artiax particles #3.2.1 color 37,78,95,100

[Repeated 3 time(s)]

> artiax particles #3.2.1 color 37,79,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,80,95,100

[Repeated 5 time(s)]

> artiax particles #3.2.1 color 37,79,95,100

> artiax particles #3.2.1 color 37,78,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,76,95,100

> artiax particles #3.2.1 color 37,73,95,100

[Repeated 3 time(s)]

> artiax particles #3.2.1 color 37,72,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,71,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,70,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.1 color 37,69,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,68,95,100

[Repeated 1 time(s)]

> artiax particles #3.2.1 color 37,67,95,100

[Repeated 2 time(s)]

> artiax particles #3.2.2 color 0,20,50,100

> artiax particles #3.2.2 color 0,46,86,100

Opened Chlamy_ko_1h_004_rec_flipped_corrected.mrc as #3.1.1, grid size
698,960,200, pixel 13.1,13.1,13.1, shown at level 0.124, step 1, values
float32  

> artiax tomo #3.1.1 sliceDirection 0,0,1

> artiax view xy

> lighting simple

> artiax tomo #3.1.1 slice 77

> artiax tomo #3.1.1 slice 81

> artiax tomo #3.1.1 slice 79

> select #3.2.3.2

1 model selected  

> artiax show markers

> select #3.2.3.3/M:12@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> ui mousemode right select

> select #3.2.3.3/M:58@M

1 atom, 1 residue, 1 model selected  

> ui mousemode right "translate selected particles"

> artiax tomo #3.1.1 slice 71

> ui mousemode right "rotate selected particles"

> ui mousemode right "translate selected particles"

> hide #!3.1.1 models

> view orient

> ui tool show "Side View"

> lighting soft

> volume #1 color #008251

> volume #1 color #007451

> volume #1 color #008a51

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

> ui mousemode right select

> select clear

> save /Users/zhenhou/Desktop/image2.png supersample 3

> artiax hide markers

[Repeated 3 time(s)]

> view

> view orient

[Repeated 1 time(s)]

> ui tool show "Side View"

> save /Users/zhenhou/Desktop/image3.png supersample 3

> view orient

[Repeated 1 time(s)]

> save /Users/zhenhou/Desktop/image3.png supersample 3

> save /Users/zhenhou/Desktop/image4.png supersample 3

> lighting simple

> lighting soft

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

> view orient

> hide #!3.2.2 models

> hide #!3.2.3 models

> hide #!3.2.1 models

> open
> /Users/zhenhou/Desktop/manuscripts/2023/Thylakoid/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_003_rec_flipped_corrected_labels_chloroplast.mrc

Opened Chlamy_ko_1h_003_rec_flipped_corrected_labels_chloroplast.mrc as #4,
grid size 698,960,200, pixel 13.1,13.1,13.1, shown at level 0.0007, step 2,
values int16  

> close #3.1.1

> volume #4 level 10.04

> volume #4 level 13.17

> volume #4 step 1

> volume #4 surfaceSmoothing true

> volume #4 smoothingIterations 50

> open
> /Users/zhenhou/Desktop/manuscripts/2023/Thylakoid/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_003_rec_flipped_corrected_labels_thylakoid.mrc

Opened Chlamy_ko_1h_003_rec_flipped_corrected_labels_thylakoid.mrc as #5, grid
size 698,960,200, pixel 13.1,13.1,13.1, shown at level 0.0007, step 2, values
int16  

> volume #5 step 1

> volume #5 level 9.71

> volume #5 surfaceSmoothing true

> volume #5 smoothingIterations 50

> open
> /Users/zhenhou/Desktop/manuscripts/2023/Thylakoid/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_003_rec_flipped_corrected_labels_pm.mrc

Opened Chlamy_ko_1h_003_rec_flipped_corrected_labels_pm.mrc as #6, grid size
698,960,200, pixel 13.1,13.1,13.1, shown at level 0.0007, step 2, values int16  

> volume #6 step 1

> volume #6 level 8.983

> volume #6 surfaceSmoothing true

> volume #6 smoothingIterations 50

> volume #4 color #c9fa98

> volume #4 color #008a51

> volume #5 color #baf688

> volume #6 color darkgrey

> view orient

> volume #6 level 10.14

> volume #5 level 10.21

> volume #6 level 10.31

> volume #6 level 13.17

> volume #5 level 13.17

> volume #4 smoothingFactor 0.5

> volume #5 smoothingFactor 0.5

> volume #6 smoothingFactor 0.5

> view orient

> volume #5 smoothingFactor 0.2

> volume #4 smoothingFactor 0.2

> view orient

> save /Users/zhenhou/Desktop/image2.png supersample 3

> open
> /Users/zhenhou/Desktop/manuscripts/2023/Thylakoid/Thylakoid_1h_seg/corrected_tomos/Chlamy_ko_1h_005_rec_flipped_corrected_labels_thylakoid.mrc

Opened Chlamy_ko_1h_005_rec_flipped_corrected_labels_thylakoid.mrc as #7, grid
size 698,960,200, pixel 13.1,13.1,13.1, shown at level 0.0035, step 2, values
int16  

> volume #7 step 1

> volume #7 level 42.88

> view orient

> volume #7 surfaceSmoothing true

> volume #7 smoothingFactor 0.2

> volume #7 smoothingIterations 50

> volume #7 color #b9f687

> save /Users/zhenhou/Desktop/image3.png supersample 3

> volume #1 color #0096ff

> volume #1 color darkgrey

> volume #1 color #929292

> volume #1 color #919191

> volume #1 color #929292

> open
> /Users/zhenhou/Desktop/manuscripts/2023/Nucleosome/class2_py/run_class001.mrc

Opened run_class001.mrc as #8, grid size 96,96,96, pixel 4.36, shown at level
0.0796, step 1, values float32  

> view orient

> volume #8 level 0.1751

> lighting simple

> volume #8 level 0.2193

> open /Users/zhenhou/Desktop/manuscripts/2023/Nucleosome/class2_py/6ESF.pdb

6ESF.pdb title:  
Nucleosome : class 1 [more info...]  
  
Chain information for 6ESF.pdb #9  
---  
Chain | Description | UniProt  
A E | histone H3.2 | H32_XENLA  
B F | histone H4 | H4_XENLA  
C G | histone H2A | Q6AZJ8_XENLA  
D H | H2B1.1 | H2B11_XENLA  
I | DNA (147-mer) |  
J | DNA (147-mer) |  
  

> hide #9 cartoons

[Repeated 1 time(s)]

> hide #9 atoms

[Repeated 1 time(s)]

> show #9 atoms

> hide #9 atoms

[Repeated 1 time(s)]

> show #9 atoms

> hide #9 cartoons

[Repeated 1 time(s)]

> hide #9 surfaces

[Repeated 3 time(s)]

> hide #9 cartoons

> artiax hide axes

> artiax hide markers

> artiax hide surfaces

> close #8

> hide #9 surfaces

[Repeated 1 time(s)]

> hide #9 cartoons

[Repeated 2 time(s)]

> view orient

> hide #9 cartoons

[Repeated 3 time(s)]

> show #9 surfaces

> hide #!9 cartoons

> show #!9 atoms

> hide #!9 cartoons

[Repeated 2 time(s)]

> hide #!9 surfaces

[Repeated 1 time(s)]

> hide #!9 atoms

[Repeated 2 time(s)]

> show #!9 atoms

[Repeated 1 time(s)]

> hide #!9 atoms

> show #!9 cartoons




OpenGL version: unknown
Could not make opengl context current

Python: 3.9.11
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: Mac14,7
      Chip: Apple M2
      Total Number of Cores: 8 (4 performance and 4 efficiency)
      Memory: 24 GB
      System Firmware Version: 7459.141.1
      OS Loader Version: 7459.141.1

Software:

    System Software Overview:

      System Version: macOS 12.5.1 (21G83)
      Kernel Version: Darwin 21.6.0
      Time since boot: 40 days 14:14

Graphics/Displays:

    Apple M2:

      Chipset Model: Apple M2
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 10
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-In Retina LCD
          Resolution: 2560 x 1600 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: Yes
          Connection Type: Internal


Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.3
    asttokens: 2.1.0
    Babel: 2.11.0
    backcall: 0.2.0
    blockdiag: 3.0.0
    build: 0.8.0
    certifi: 2021.10.8
    cftime: 1.6.2
    charset-normalizer: 2.1.1
    ChimeraX-AddCharge: 1.4
    ChimeraX-AddH: 2.2.1
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2.1
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.6
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.3
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-ArtiaX: 0.3
    ChimeraX-Atomic: 1.41.5
    ChimeraX-AtomicLibrary: 8.0.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3
    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: 2.7.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.1
    ChimeraX-ChangeChains: 1.0.2
    ChimeraX-CheckWaters: 1.3
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.2
    ChimeraX-CommandLine: 1.2.4
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.5
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.1
    ChimeraX-DistMonitor: 1.3
    ChimeraX-DockPrep: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.2
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 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: 1.1.2
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.1
    ChimeraX-MatchMaker: 2.0.9
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.8
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.6
    ChimeraX-ModelPanel: 1.3.6
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.1
    ChimeraX-MouseModes: 1.1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.9.1
    ChimeraX-PDB: 2.6.8
    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-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.1
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 2.0.1
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.7.2
    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
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.1.3
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.1
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.24.3
    ChimeraX-uniprot: 2.2.1
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.1.4
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.1
    ChimeraX-WebServices: 1.1.0
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.5
    cxservices: 1.2
    cycler: 0.11.0
    Cython: 0.29.32
    debugpy: 1.6.4
    decorator: 5.1.1
    docutils: 0.19
    entrypoints: 0.4
    executing: 1.2.0
    filelock: 3.7.1
    fonttools: 4.38.0
    funcparserlib: 1.0.1
    geomdl: 5.3.1
    grako: 3.16.5
    h5py: 3.7.0
    html2text: 2020.1.16
    idna: 3.4
    ihm: 0.33
    imagecodecs: 2022.7.31
    imagesize: 1.4.1
    importlib-metadata: 5.1.0
    ipykernel: 6.15.3
    ipython: 8.4.0
    ipython-genutils: 0.2.0
    jedi: 0.18.1
    Jinja2: 3.1.2
    jupyter-client: 7.3.4
    jupyter-core: 5.1.0
    kiwisolver: 1.4.4
    line-profiler: 3.5.1
    lxml: 4.9.1
    lz4: 4.0.2
    MarkupSafe: 2.1.1
    matplotlib: 3.5.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.6
    netCDF4: 1.6.0
    networkx: 2.8.5
    numexpr: 2.8.4
    numpy: 1.23.1
    openvr: 1.23.701
    packaging: 21.3
    pandas: 1.5.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 9.2.0
    pip: 22.2.2
    pkginfo: 1.8.3
    platformdirs: 2.5.4
    prompt-toolkit: 3.0.33
    psutil: 5.9.1
    ptyprocess: 0.7.0
    pure-eval: 0.2.2
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.12.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.9
    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: 2022.6
    pyzmq: 24.0.1
    qtconsole: 5.3.1
    QtPy: 2.3.0
    RandomWords: 0.4.0
    requests: 2.28.1
    scipy: 1.9.0
    setuptools: 65.1.1
    setuptools-scm: 7.0.5
    sfftk-rw: 0.7.2
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 5.1.1
    sphinx-autodoc-typehints: 1.19.1
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.2
    sphinxcontrib-htmlhelp: 2.0.0
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.3
    sphinxcontrib-serializinghtml: 1.1.5
    stack-data: 0.6.2
    starfile: 0.4.11
    superqt: 0.4.1
    tables: 3.7.0
    tifffile: 2022.7.31
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.2
    traitlets: 5.3.0
    typing-extensions: 4.4.0
    urllib3: 1.26.13
    wcwidth: 0.2.5
    webcolors: 1.12
    wheel: 0.37.1
    wheel-filename: 1.4.1
    zipp: 3.11.0

[pett]

Duplicate of #8706