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