The primary ISOLDE object

class chimerax.isolde.isolde.IsoldeParams(**kw)

Contains the basic settings for defining and displaying the atoms and maps involved in an interactive simulation. Changes to parameter values will affect all future simulations in the ISOLDE session. At present, permanent changes can only be made by editing the corresponding entry in constants.py.

class chimerax.isolde.isolde.Isolde(session, gui=None)

The master ISOLDE class, primarily designed to be used by the ISOLDE GUI as the front-end interface for starting, controlling and analysing interactive simulations. Should only be used as a session-level singleton. Once initialised will be accessible as session.isolde.

__init__(session, gui=None)

Initialises the ISOLDE object and adds it to the ChimeraX session as session.isolde.

Args:
  • gui (default=None):

    • Used by the ISOLDE BundleAPI to prepare the ISOLDE GUI interface (i.e. when running from Tools/General/ISOLDE in the ChimeraX GUI menu).

add_checkpoint_block(obj, reason)

Some processes are incompatible with checkpointing. We need to know when these are running and disable checkpointing until they’re done.

Args:
  • obj:

    • The Python object blocking checkpointing

  • reason:

    • A text string.

property can_checkpoint

Is checkpoint save/revert currently allowed?

change_selected_model(model)

Change the model upon which ISOLDE is focused (that is, upon which simulations will be run). This performs some basic preparations, including preparing any maps associated with the model for simulation. While ISOLDE is running, only atoms from the selected model will be selectable using the mouse.

Args:
  • model:

    • a chimerax.AtomicStructure instance.

checkpoint(*_)

Save the current state of the simulation (coordinates and all restraints).

commit_sim()

Stop the simulation and keep the current coordinates.

discard_sim(revert_to='checkpoint', warn=True)

Stop the simulation and revert to either the starting state or the last saved checkpoint.

Args:
  • revert_to (default: ‘checkpoint’):

    • Either ‘checkpoint’ or ‘start’

  • warn (default: True):

    • if warn is True and checkpoint==’start’, a warning dialog will be raised allowing the user to back out before discarding the simulation coordinates.

equilibrate()

Switch the imulation to equilibration mode

flip_peptide_bond(res)

Flip the peptide bond N-terminal to the given residue by the addition of temporary phi/psi restraints. Requires a simulation to be running.

Args:
  • res:

    • A ChimeraX Residue instance

flip_peptide_omega(res)

Flip the peptide bond N-terminal to this residue from cis to trans or vice versa. Only usable when a simulation is running.

Args:
  • res:

    • A chimerax.Residue instance pointing to a non-N-terminal amino acid residue.

property ignored_residues

A chimerax.Residues object defining residues to be ignored for simulation purposes. Residues in this list will be retained in the model and used for map calculations, but will not be included in simulations. In most cases, this should only be populated with residues that have not been parameterised for MD.

load_model_and_data(model_file, mtzfile)

Load a model and MTZ file ready for simulation

Args:
  • model_file:

    • a PDB or mmCIF file

  • mtzfile:

    • a MTZ file containing experimental F/sigF and/or precalculated F/phi columns.

minimize()

Switch the simulation to energy minimisation mode

params

A IsoldeParams instance containing basic parameters controlling how the interactive simulation selection is defined and displayed.

pause()

If simulation is currently running, pause it. Otherwise, do nothing.

pause_sim_toggle()

Pause/resume the simulation

remove_checkpoint_block(obj)

Release a block on checkpointing. When all blocks are removed, checkpointing will be re-enabled.

Args:
  • obj:

    • the Python object no longer blocking checkpointing

reset_sim_params()

Reset all the simulation parameters back to the defaults found in constants.py.

resume()

If an active simulation is currently paused, resume it. Otherwise, do nothing.

revert_to_checkpoint(*_)

Return the simulation to the last saved checkpoint. Note: a checkpoint is automatically saved at the beginning of each simulation.

property selected_atoms

Returns the set of selected atoms in ISOLDE’s currently selected model. If ISOLDE has no model currently selected, returns an empty Atoms object.

property selected_model

Returns the atomic model on which ISOLDE is currently operating. Can be set.

property selected_model_has_maps

Returns True if the selected model has at least one map associated with it, otherwise False. Read only.

property selected_model_has_mdff_enabled

Returns True if the selected model has at least one MDFF manager present and enabled for MDFF fitting, otherwise False. Read only

show_master_help_in_browser(*_)

Open the ISOLDE help documentation.

property sim_handler

Returns the isolde.openmm.SimHandler instance controlling the currently running simulation, or None if no simulation is running. Read only.

property sim_manager

Returns the isolde.openmm.SimManager instance providing high-level control over the current simulation. If no simulation is currently defined, returns None. Read only.

property sim_paused

Returns True if the simulation is paused or no simulation is running, otherwise False.

property simulation_mode

Returns ‘equil’ or ‘min’ depending on the state of the simulation, or None if no simulation is defined. Read only. To switch modes, use isolde.minimize() and :func@`isolde.equilibrate`.

property simulation_running

Returns True if a simulation is running, otherwise False. Read only.

property smoothing

Turn smoothing of the simulation trajectory visualisation on or off.

property smoothing_alpha

Get/set the value of the constant defining how heavily smoothed the trajectory visualisation is. Value must be greater than zero and less than or equal to one. A value of 1 indicates no smoothing, while a value of 0.01 indicates that a given frame contributes only 1% to the displayed moving average.

start_sim()

Start an interactive simulation based around the currently-selected atoms.

stop_tugging(atom_or_atoms)

Release one or more atoms from the tugging force.

Args:
  • atom_or_atoms:

    • A chimerax.Atom or Atoms instance

tug_atom_to(atom, target, spring_constant=None)

Tug an atom towards the given target coordinates in the context of a running simulation. If no spring constant is given, a default value will be used. NOTE: the tugging effect will remain in place until updated with a new call to tug_atom_to() or removed with stop_tugging(atom).

Args:
  • atom:

    • The atom to be tugged. Must be a heavy atom that is mobile in the current simulation

  • target:

    • An iterable giving the (x,y,z) target in Angstroms

  • spring constant (default None):

    • An optional spring constant (in kJ mol-1 A-2). If none is provided, the default in sim_params.mouse_tug_spring_constant will be used.