Re: [chimerax-users] Scenes

[joseph.boyle@…]

I used to be involved in Molecular Dynamics (MD) simulations. It struck me that our central question - whether a ligand could fit in a cavity of an active site allowing for induced fit / protein flexibility - i.e. a larger active site than the unliganded crystal structure - could be answered more efficiently.

Specifically, MD is essentially intended to simulate thermal motions and basically increments bond angles. Whereas we were really asking about energy of some conformations (the ones with the enlarged active site). Indeed there are similar approaches in the literature e.g. Markov Monte Carlo - so it's not crazy ! This approach would promise to be much more computationally efficient than MD.

I am wondering if it is possible to use ChimeraX (or Chimera) to step-change the bond angles to enlarge the active site and recalculate energy and ligand dock - possibly in Python using a reiterative script ?

Hope my description is clear ?


Joseph J. Boyle

B.Sc.(Pharmacol. Hons Class I Glasgow), M.B.Ch.B.(with Hons Glasgow), Ph.D. (Cambridge), F.R.C.Path.(Histopath.),

Professor of Chemical Systems Pathology

National Heart and Lung Institute

Deputy Lead for Information Governance Faculty of Medicine

Imperial College London


Address:

Office 513

National Heart and Lung Institute

Dr Victor Phillip Dahdaleh Building (VPD Building)

Imperial College London, Hammersmith Campus

Du Cane Rd

London

W12 0NN

UK


________________________________
From: Timothy Springer via ChimeraX-users <chimerax-users@cgl.ucsf.edu>
Sent: 05 February 2026 13:42
To: chimerax-bugs@cgl.ucsf.edu <chimerax-bugs@cgl.ucsf.edu>; ChimeraX Users Help <chimerax-users@cgl.ucsf.edu>
Subject: [chimerax-users] Scenes


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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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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<http://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