Opened 3 years ago

Closed 3 years ago

#8082 closed defect (can't reproduce)

Volume not in Surface Color volume menu

Reported by: chimerax-bug-report@… Owned by: Eric Pettersen
Priority: normal Milestone:
Component: UI Version:
Keywords: Cc: Tom Goddard
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        macOS-10.16-x86_64-i386-64bit
ChimeraX Version: 1.3 (2021-12-08 23:08:33 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/chenmengying/Desktop/P2_projects/ClassI_P2F604P_MLSA1_res.cxs
> format session

Opened half1_resmap.mrc as #4, grid size 240,240,240, pixel 1.09, shown at
level 100, step 1, values float32  
Opened postrun4newK1K25.mrc as #2, grid size 240,240,240, pixel 1.09, shown at
level 0.0219, step 1, values float32  
Log from Mon Nov 21 21:25:09 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Users/chenmengying/Desktop/P2_projects/ClassII_P2F604P_MLSA1_res.cxs

Opened 3.0_run6K2.mrc as #1, grid size 240,240,240, pixel 1.09, shown at level
0.0193, step 1, values float32  
Opened half1_resmap.mrc as #2, grid size 240,240,240, pixel 1.09, shown at
level 2.4, step 1, values float32  
Log from Fri Nov 18 20:41:18 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  

> open /Volumes/DORAEYING/PKD2F604P_Drug/drafts/Res_P2_604P_200um.cxs

Opened 3.0_run6K2.mrc as #1, grid size 240,240,240, pixel 1.09, shown at level
0.0193, step 1, values float32  
Opened half1_resmap.mrc as #2, grid size 240,240,240, pixel 1.09, shown at
level 2.4, step 1, values float32  
Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  
Log from Sat Oct 29 20:31:43 2022UCSF ChimeraX version: 1.3 (2021-12-08)  
© 2016-2021 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Volumes/DORAEYING/PKD2F604P_Drug/3.0_run6K2.mrc

Opened 3.0_run6K2.mrc as #1, grid size 240,240,240, pixel 1.09, shown at level
0.0135, step 1, values float32  

> open /Users/chenmengying/Desktop/half1_resmap.mrc

Opened half1_resmap.mrc as #2, grid size 240,240,240, pixel 1.09, shown at
level 100, step 1, values float32  

> set bgColor white

> lighting soft

> volume #1 level 0.01951

> volume #2 level 100

> volume #2 level 2.4

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette #ff0000:#ffffff:#0000ff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#ff0000:3,#ffffff:3.5,#0000ff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#0000ff:3,#00b1ff:3.5,#84caff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#0000ff:3,#00b1ff:3.5,#84caff:4,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> ui tool show "Hide Dust"

> surface dust #1 size 5

[Repeated 1 time(s)]

> ui tool show "Hide Dust"

> surface dust #1 size 10

[Repeated 1 time(s)]

> color sample #1.1 map #2 palette 2.5,#0042ff:3,#00b1ff:3.5,#84caff:4,#ff272f

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#0042ff:3,#00b1ff:3.5,#84caff:4,#ff275d

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#e2baff:3,#00b1ff:3.5,#84caff:4,#ff275d

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#e2baff:3,#00b1ff:3.5,#84caff:4,#0000ff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#ffc8ff:3,#70b1ff:3.5,#84caff:4,#0000ff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#ffc8ff:3,#70b1ff:3.5,#84caff:4,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#ffdbff:3,#70b1ff:3.5,#84caff:4,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#ffdbff:3,#9db1ff:3.5,#84caff:4,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#ffdbff:3,#9db1ff:3.5,#84caff:4,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#ffbcff:3,#f5e0ff:3.5,#a7caff:4,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#4e73ff:3,#81d1ff:3.5,#ffffff:4,#ffe5ff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#0014ff:3,#81d1ff:3.5,#ffffff:4,#ffe5ff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#1968ff:3,#81d1ff:3.5,#ffffff:4,#ffe5ff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> color sample #1.1 map #2 palette 2.5,#1968ff:3,#8ed1ff:3.5,#ffffff:4,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.873, maximum 100  

> volume #1 level 0.01928

> color sample #1.1 map #2 palette 2.5,#75b5ff:3,#8ed1ff:3.5,#ffffff:4,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2.5,#75b5ff:3,#a9d1ff:3.5,#ffffff:4,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2.5,#75b5ff:3,#a9d1ff:3.5,#ffffff:4,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> lighting soft

> lighting full

> lighting soft

> lighting simple

> lighting soft

> set bgColor white

> set bgColor black

> set bgColor white

> color sample #1.1 map #2 palette 2.5,#75ffff:3,#a9d1ff:3.5,#ffffff:4,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2.5,#0d82ff:3,#a9ffff:3.5,#ffffff:4,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2.5,#0d82ff:3,#a9ffff:3.5,#ffffff:4,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d82ff:3.5,#a9ffff:3,#ffffff:3.5,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d82ff:2.5,#a9ffff:3,#ffffff:3.5,#ffcdff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d82ff:2.5,#a9ffff:3,#ffffff:3.5,#ff0000

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d82ff:2.5,#a9ffff:3,#ffffff:3.5,#ffb4d1

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d82ff:2.5,#a9ffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d39ff:2.5,#a9ffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d00ff:2.5,#a9ffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d00ff:2.5,#a9ffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d00ff:2.5,#ccffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0d92ff:2.5,#ccffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000ff:2.5,#79ffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000ff:2.5,#aaffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000ff:2.5,#aaffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000ff:2.5,#b4ffff:3,#ffffff:3.5,#ffdbff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000ff:2.5,#b4ffff:3,#ffffff:3.5,#ffa6ff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000ff:2.5,#b4ffff:3,#ffffff:3.5,#ffd3ff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000ff:2.5,#b9ffff:3,#ffffff:3.5,#ff0000

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#77e7de:2.5,#aafdff:3,#ffffff:3.5,#cf91e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#77e7de:2.5,#aafdff:3,#ffffff:3.5,#cfa0e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#77e7de:2.5,#aafdff:3,#ffffff:3.5,#80a0e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#7794de:2.5,#aafdff:3,#ffffff:3.5,#80a0e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#7794de:2.5,#aafdff:3,#ffffff:3.5,#ffa0e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#7794de:2.5,#d3fdff:3,#ffffff:3.5,#ffa0e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000de:2.5,#d3fdff:3,#ffffff:3.5,#ffc4e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000de:2.5,#89fdff:3,#ffffff:3.5,#ffc4e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette 2,#0000de:2.5,#89fdff:3,#ffffff:3.5,#ffc4e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color single #1.1

> key #0000de:2.0 #89fdff:2.5 white:3.0 #ffc4e4:3.5 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color sample #1.1 map #2 palette 2,#0000de:2.5,#89fdff:3,#ffffff:3.5,#ffc4e4

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> ui tool show "Side View"

> save /Users/chenmengying/Desktop/Res_P2_604P_200um.cxs includeMaps true

——— End of log from Sat Oct 29 20:31:43 2022 ———

opened ChimeraX session  

> ui tool show "Surface Color"

> color sample #1.1 map #2 palette 2,#004aff:2.5,#89fdff:3,#dcffff:3.5,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette
> 2.8,#004aff:3.3,#89fdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> key #004aff:2.8 #89fdff:3.3 #dcffff:3.8 white:4.3 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> color sample #1.1 map #2 palette
> 2.8,#004aff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette
> 2.8,#004aff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette
> 2.8,#004aff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette
> 2.8,#004aff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette
> 2.8,#0000ff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette
> 2.8,#004aff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette
> 2.8,#004aff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> color sample #1.1 map #2 palette
> 2.8,#004aff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 2.913, maximum 100  

> key #004aff:2.8 #8afdff:3.3 #dcffff:3.8 white:4.3 showTool true

> ui mousemode right "color key"

> ui mousemode right translate

> save /Users/chenmengying/Desktop/P2_projects/resloc_classII.png width 4000
> height 3071 supersample 3

> save /Users/chenmengying/Desktop/P2_projects/ClassII_P2F604P_MLSA1_res.cxs
> includeMaps true

——— End of log from Fri Nov 18 20:41:18 2022 ———

opened ChimeraX session  

> open /Users/chenmengying/Desktop/half1_resmap.mrc

Opened half1_resmap.mrc as #4, grid size 240,240,240, pixel 1.09, shown at
level 100, step 1, values float32  

> close #2

> open /Users/chenmengying/Desktop/postrun4newK1K25.mrc

Opened postrun4newK1K25.mrc as #2, grid size 240,240,240, pixel 1.09, shown at
level 0.0135, step 1, values float32  

> volume #2 level 0.02194

> ui tool show "Surface Color"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1264, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/__init__.py", line 93, in start_tool  
ti = surfcolorgui.show_surface_color_panel(session)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 697, in
show_surface_color_panel  
return surface_color_panel(session, create = True)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 692, in surface_color_panel  
return SurfaceColorGUI.get_singleton(session, create=create)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 76, in get_singleton  
return tools.get_singleton(session, SurfaceColorGUI, 'Surface Color',  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 64, in __init__  
self._surface_chosen()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 377, in _surface_chosen  
self._map.value = sc.volume  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 391, in _set_value  
self._menu.value = value  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 341, in value  
self.set_value(val)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 363, in set_value  
self.setText(self.value_map[val])  
KeyError: <chimerax.map.volume.Volume object at 0x7f84a9fec1c0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1659, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Surface
Color in bundle ChimeraX-Surface:  
<chimerax.map.volume.Volume object at 0x7f84a9fec1c0>  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Surface
Color in bundle ChimeraX-Surface:  
  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> ui tool show "Surface Color"

[Repeated 2 time(s)]Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1264, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/__init__.py", line 93, in start_tool  
ti = surfcolorgui.show_surface_color_panel(session)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 697, in
show_surface_color_panel  
return surface_color_panel(session, create = True)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 692, in surface_color_panel  
return SurfaceColorGUI.get_singleton(session, create=create)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 76, in get_singleton  
return tools.get_singleton(session, SurfaceColorGUI, 'Surface Color',  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 64, in __init__  
self._surface_chosen()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 377, in _surface_chosen  
self._map.value = sc.volume  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 391, in _set_value  
self._menu.value = value  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 341, in value  
self.set_value(val)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 363, in set_value  
self.setText(self.value_map[val])  
KeyError: <chimerax.map.volume.Volume object at 0x7f84a9fec1c0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1659, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Surface
Color in bundle ChimeraX-Surface:  
<chimerax.map.volume.Volume object at 0x7f84a9fec1c0>  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Surface
Color in bundle ChimeraX-Surface:  
  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  

> close #1

> ui tool show "Surface Color"

> color sample #2.1 map #4 palette
> 2.8,#004aff:3.3,#8afdff:3.8,#dcffff:4.3,#ffffff

Map values for surface "surface": minimum 2.4, mean 3.779, maximum 100  
Map values for surface "cap far": minimum 4.394, mean 4.418, maximum 4.615  

> ui tool show "Hide Dust"

> tile

2 models tiled  

> tile

2 models tiled  

> surface dust #2 size 6.52

> save /Users/chenmengying/Desktop/P2_projects/resloc_classI.png width 4000
> height 3110 supersample 3

> save /Users/chenmengying/Desktop/P2_projects/ClassI_P2F604P_MLSA1_res.cxs
> includeMaps true

——— End of log from Mon Nov 21 21:25:09 2022 ———

opened ChimeraX session  

> close #4

> open /Users/chenmengying/Desktop/i_half1_resmap.mrc

Opened i_half1_resmap.mrc as #1, grid size 240,240,240, pixel 1.09, shown at
level 100, step 1, values float32  

> ui tool show "Surface Color"

Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 554, in start_tool  
ti = api._api_caller.start_tool(api, session, self, tool_info)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/__init__.py", line 1264, in start_tool  
return cls._get_func(api, "start_tool")(session, ti.name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/__init__.py", line 93, in start_tool  
ti = surfcolorgui.show_surface_color_panel(session)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 697, in
show_surface_color_panel  
return surface_color_panel(session, create = True)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 692, in surface_color_panel  
return SurfaceColorGUI.get_singleton(session, create=create)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 76, in get_singleton  
return tools.get_singleton(session, SurfaceColorGUI, 'Surface Color',  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/tools.py", line 193, in get_singleton  
tinst = tool_class(session, tool_name, **kw)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 64, in __init__  
self._surface_chosen()  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/surface/surfcolorgui.py", line 377, in _surface_chosen  
self._map.value = sc.volume  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/composite.py", line 391, in _set_value  
self._menu.value = value  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 341, in value  
self.set_value(val)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/widgets/item_chooser.py", line 363, in set_value  
self.setText(self.value_map[val])  
KeyError: <chimerax.map.volume.Volume object at 0x7fe1983142e0>  
  
During handling of the above exception, another exception occurred:  
  
Traceback (most recent call last):  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/gui.py", line 1659, in <lambda>  
run(ses, "ui tool show %s" % StringArg.unparse(tool_name)))  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/run.py", line 36, in run  
results = command.run(text, log=log, return_json=return_json)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/commands/cli.py", line 2856, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/ui/cmd.py", line 219, in ui_tool_show  
bi.start_tool(session, name)  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Surface
Color in bundle ChimeraX-Surface:  
<chimerax.map.volume.Volume object at 0x7fe1983142e0>  
  
chimerax.core.toolshed.ToolshedError: start_tool() failed for tool Surface
Color in bundle ChimeraX-Surface:  
  
  
File
"/Applications/ChimeraX-1.3.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-
packages/chimerax/core/toolshed/info.py", line 559, in start_tool  
raise ToolshedError(  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 Metal - 76.1
OpenGL renderer: Apple M1 Pro
OpenGL vendor: AppleHardware:

    Hardware Overview:

      Model Name: MacBook Pro
      Model Identifier: MacBookPro18,3
      Processor Name: Unknown
      Processor Speed: 2.4 GHz
      Number of Processors: 1
      Total Number of Cores: 8
      L2 Cache: 16 MB
      Memory: 16 GB

Software:

    System Software Overview:

      System Version: macOS 12.0.1 (21A559)
      Kernel Version: Darwin 21.1.0
      Time since boot: 3 days 2:23

Graphics/Displays:

    Apple G13X:

      Chipset Model: Apple G13X
      Type: GPU
      Bus: Built-In
      Total Number of Cores: 14
      Vendor: Apple (0x106b)
      Metal Family: Supported, Metal GPUFamily Apple 7
      Displays:
        Color LCD:
          Display Type: Built-in Liquid Retina XDR Display
          Resolution: 3024 x 1964 Retina
          Main Display: Yes
          Mirror: Off
          Online: Yes
          Automatically Adjust Brightness: No
          Connection Type: Internal

Locale: (None, 'UTF-8')
PyQt5 5.15.2, Qt 5.15.2
Installed Packages:
    alabaster: 0.7.12
    appdirs: 1.4.4
    appnope: 0.1.2
    Babel: 2.9.1
    backcall: 0.2.0
    blockdiag: 2.0.1
    certifi: 2021.5.30
    cftime: 1.5.1.1
    charset-normalizer: 2.0.9
    ChimeraX-AddCharge: 1.2.2
    ChimeraX-AddH: 2.1.11
    ChimeraX-AlignmentAlgorithms: 2.0
    ChimeraX-AlignmentHdrs: 3.2
    ChimeraX-AlignmentMatrices: 2.0
    ChimeraX-Alignments: 2.2.3
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.0.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.0
    ChimeraX-Atomic: 1.31
    ChimeraX-AtomicLibrary: 4.2
    ChimeraX-AtomSearch: 2.0
    ChimeraX-AtomSearchLibrary: 1.0
    ChimeraX-AxesPlanes: 2.0
    ChimeraX-BasicActions: 1.1
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.0
    ChimeraX-BondRot: 2.0
    ChimeraX-BugReporter: 1.0
    ChimeraX-BuildStructure: 2.6.1
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.1
    ChimeraX-ButtonPanel: 1.0
    ChimeraX-CageBuilder: 1.0
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.2
    ChimeraX-ChemGroup: 2.0
    ChimeraX-Clashes: 2.2.2
    ChimeraX-ColorActions: 1.0
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5
    ChimeraX-CommandLine: 1.1.5
    ChimeraX-ConnectStructure: 2.0
    ChimeraX-Contacts: 1.0
    ChimeraX-Core: 1.3
    ChimeraX-CoreFormats: 1.1
    ChimeraX-coulombic: 1.3.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0
    ChimeraX-DataFormats: 1.2.2
    ChimeraX-Dicom: 1.0
    ChimeraX-DistMonitor: 1.1.5
    ChimeraX-DistUI: 1.0
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ExperimentalCommands: 1.0
    ChimeraX-FileHistory: 1.0
    ChimeraX-FunctionKey: 1.0
    ChimeraX-Geometry: 1.1
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1
    ChimeraX-Hbonds: 2.1.2
    ChimeraX-Help: 1.2
    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
    ChimeraX-Label: 1.1
    ChimeraX-ListInfo: 1.1.1
    ChimeraX-Log: 1.1.4
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.8.1
    ChimeraX-Map: 1.1
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0
    ChimeraX-MapFilter: 2.0
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1
    ChimeraX-Markers: 1.0
    ChimeraX-Mask: 1.0
    ChimeraX-MatchMaker: 2.0.4
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.1
    ChimeraX-Meeting: 1.0
    ChimeraX-MLP: 1.1
    ChimeraX-mmCIF: 2.4
    ChimeraX-MMTF: 2.1
    ChimeraX-Modeller: 1.2.6
    ChimeraX-ModelPanel: 1.2.1
    ChimeraX-ModelSeries: 1.0
    ChimeraX-Mol2: 2.0
    ChimeraX-Morph: 1.0
    ChimeraX-MouseModes: 1.1
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nucleotides: 2.0.2
    ChimeraX-OpenCommand: 1.7
    ChimeraX-PDB: 2.6.5
    ChimeraX-PDBBio: 1.0
    ChimeraX-PDBLibrary: 1.0.2
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.0.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1
    ChimeraX-RemoteControl: 1.0
    ChimeraX-ResidueFit: 1.0
    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
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.4.6
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0
    ChimeraX-Shortcuts: 1.1
    ChimeraX-ShowAttr: 1.0
    ChimeraX-ShowSequences: 1.0
    ChimeraX-SideView: 1.0
    ChimeraX-Smiles: 2.1
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.6.1
    ChimeraX-STL: 1.0
    ChimeraX-Storm: 1.0
    ChimeraX-Struts: 1.0
    ChimeraX-Surface: 1.0
    ChimeraX-SwapAA: 2.0
    ChimeraX-SwapRes: 2.1
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1
    ChimeraX-ToolshedUtils: 1.2
    ChimeraX-Tug: 1.0
    ChimeraX-UI: 1.13.7
    ChimeraX-uniprot: 2.2
    ChimeraX-UnitCell: 1.0
    ChimeraX-ViewDockX: 1.0.1
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0
    ChimeraX-WebServices: 1.0
    ChimeraX-Zone: 1.0
    colorama: 0.4.4
    cxservices: 1.1
    cycler: 0.11.0
    Cython: 0.29.24
    decorator: 5.1.0
    docutils: 0.17.1
    filelock: 3.0.12
    funcparserlib: 0.3.6
    grako: 3.16.5
    h5py: 3.6.0
    html2text: 2020.1.16
    idna: 3.3
    ihm: 0.21
    imagecodecs: 2021.4.28
    imagesize: 1.3.0
    ipykernel: 5.5.5
    ipython: 7.23.1
    ipython-genutils: 0.2.0
    jedi: 0.18.0
    Jinja2: 3.0.1
    jupyter-client: 6.1.12
    jupyter-core: 4.9.1
    kiwisolver: 1.3.2
    lxml: 4.6.3
    lz4: 3.1.3
    MarkupSafe: 2.0.1
    matplotlib: 3.4.3
    matplotlib-inline: 0.1.3
    msgpack: 1.0.2
    netCDF4: 1.5.7
    networkx: 2.6.3
    numexpr: 2.8.0
    numpy: 1.21.2
    openvr: 1.16.801
    packaging: 21.0
    ParmEd: 3.2.0
    parso: 0.8.3
    pexpect: 4.8.0
    pickleshare: 0.7.5
    Pillow: 8.3.2
    pip: 21.2.4
    pkginfo: 1.7.1
    prompt-toolkit: 3.0.23
    psutil: 5.8.0
    ptyprocess: 0.7.0
    pycollada: 0.7.1
    pydicom: 2.1.2
    Pygments: 2.10.0
    PyOpenGL: 3.1.5
    PyOpenGL-accelerate: 3.1.5
    pyparsing: 3.0.6
    PyQt5-commercial: 5.15.2
    PyQt5-sip: 12.8.1
    PyQtWebEngine-commercial: 5.15.2
    python-dateutil: 2.8.2
    pytz: 2021.3
    pyzmq: 22.3.0
    qtconsole: 5.1.1
    QtPy: 1.11.3
    RandomWords: 0.3.0
    requests: 2.26.0
    scipy: 1.7.1
    setuptools: 57.5.0
    sfftk-rw: 0.7.1
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    Sphinx: 4.2.0
    sphinx-autodoc-typehints: 1.12.0
    sphinxcontrib-applehelp: 1.0.2
    sphinxcontrib-blockdiag: 2.0.0
    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
    suds-jurko: 0.6
    tifffile: 2021.4.8
    tinyarray: 1.2.3
    tornado: 6.1
    traitlets: 5.1.1
    urllib3: 1.26.7
    wcwidth: 0.2.5
    webcolors: 1.11.1
    wheel: 0.37.0
    wheel-filename: 1.3.0

Change History (2)

comment:1 by Eric Pettersen, 3 years ago

Cc: Tom Goddard added
Component: Unassigned → UI
Owner: set to Eric Pettersen
Platform: → all
Project: → ChimeraX
Status: new → accepted
Summary: ChimeraX bug report submission → Volume not in Surface Color volume menu

comment:2 by Eric Pettersen, 3 years ago

Resolution: → can't reproduce
Status: accepted → closed

Seems to imply that the map is not in session.models or that it is not an instance of Volume.

The item-chooser code has changed since the version use here, so let's see if one comes in with the current code -- preferably not anonymously.

Note: See TracTickets for help on using tickets.