Scenes

[springer@…]

Scenes has a bug with centroids in a .cxc file. When I omit the centroids,
scenes works fine.

8 hydrogen bonds found
define centroid #1/A:214@CD1,CD2,CE1,CE2,CG,CZ radius 0.01
Centroid 'centroid' placed at [216.18133333 173.87416667 191.88966667]
close #3.1
distance #1.3 #1/V:38@NE2 color black dashes 6 radius 0.04
Distance between a4b1_12G10_VCAMD1D3_core_122_real_space_refined_123.pdb
#!1/V GLN 38 NE2 and centroid #1.3: 3.474Å
define centroid #2/A:214@CD1,CD2,CE1,CE2,CG,CZ radius 0.01
Centroid 'centroid' placed at [215.46366667 173.33033333 193.372 ]
show :Mg
color :Ca yellow
style :Ca, Mg sphere
Changed 12 atom styles
size :CA, Mg atomRadius +0.5
Changed 12 atom radii
color :Ca yellow
color :Mg gray
select clear
windowsize 946 1210
view matrix camera
0.61619,-0.78632,0.04465,217.04,0.17445,0.080986,-0.98133,138.47,0.76803,0.61248,0.18708,205.73
view matrix models
#1,1,0,0,0,0,1,0,0,0,0,1,0,#1.1,1,0,0,0,0,1,0,0,0,0,1,0,#1.2,1,0,0,0,0,1,0,0,0,0,1,0,#2,0.99998,0.0014978,0.0060567,-0.7471,-0.0012816,0.99937,-0.035532,7.7363,-0.0061061,0.035524,0.99935,-6.4316,#2.1,1,0,0,0,0,1,0,0,0,0,1,0,#2.2,1,0,0,0,0,1,0,0,0,0,1,0
scenes save vcam_inter
scenes restore vcam_inter
Traceback (most recent call last):
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 816, in dropEvent
    _open_dropped_file(self.session, p)
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py",
line 2202, in _open_dropped_file
    run(session, 'open %s' % FileNameArg.unparse(path))
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py",
line 49, in run
    results = command.run(text, log=log, return_json=return_json)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py",
line 3237, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py",
line 132, in cmd_open
    models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py",
line 3237, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py",
line 216, in provider_open
    models, status = collated_open(session, None, [data], data_format,
_add_models,

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py",
line 510, in collated_open
    return remember_data_format()
           ^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/open_command/cmd.py",
line 498, in remember_data_format
    models, status = func(*func_args, **func_kw)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core_formats/__init__.py",
line 48, in open
    return open_command_script(session, data, file_name, **kw)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py",
line 171, in open_command_script
    _run_commands(session, commands, directory = dirname(path), log = log)
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/scripting.py",
line 184, in _run_commands
    run(session, cmd, log=log)
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/run.py",
line 49, in run
    results = command.run(text, log=log, return_json=return_json)
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/commands/cli.py",
line 3237, in run
    result = ci.function(session, **kw_args)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/cmd.py",
line 61, in restore_scene
    session.scenes.restore_scene(scene_name)
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/manager.py",
line 102, in restore_scene
    self.get_scene(scene_name).restore_scene()
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/scenes/scene.py",
line 198, in restore_scene
    model.restore_scene(scene_data)
  File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py",
line 273, in restore_scene
    Model.restore_scene(self, scene_data['model state'])
                              ~~~~~~~~~~^^^^^^^^^^^^^^^
KeyError: 'model state'

KeyError: 'model state'

File "/opt/sbgrid/i386-mac/chimerax/1.11/
ChimeraX-1.11.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/atomic/structure.py",
line 273, in restore_scene
Model.restore_scene(self, scene_data['model state'])
~~~~~~~~~~^^^^^^^^^^^^^^^
- Tim
*Timothy A. Springer, Ph.D.*
Latham Family Professor, Harvard Medical School and Boston Children's
Hospital
Founder, Institute for Protein Innovation