Live Structure Validation

General Principles

One of the core design principles underlying ISOLDE is the need for real-time, continuous and visually-clear feedback. When you are working on a structure with thousands of residues, having to stop and generate a table or plot to tell you how you did, then navigate back to each outlier and attempt to fix it before repeating the process is simply too slow, and leads people to give up while their structure is still far from perfect. The aim in ISOLDE is to instead continually show you how you’re going right now by directly marking up problems where and when they occur, telling you directly whether your manipulations are making things better or worse.

RamaAnnotator

class chimerax.isolde.validation.RamaAnnotator(atomic_structure, hide_favored=False, ignore_ribbon_hides=True)

Handles the task of real-time Ramachandran validation for a single chimerax.AtomicStructure and visualisation of the results. Results are displayed as coloured spheres overlaying the alpha carbon atoms, shading from (by default) green through yellow to hot pink as the Ramachandran score goes from favoured through allowed to outlier.

Designed to be mostly “fire-and-forget”:

ra = RamaAnnotator(atomic_structure)

adds the :py:class`RamaAnnotator` as a child model to atomic_structure and will update its validation drawing every time the coordinates change. Alternatively:

from chimerax.isolde import session_extensions as sx
ra = sx.get_rama_annotator(atomic_model)

creates the RamaAnnotator if it doesn’t exist, or returns the existing one if it does.

Turning off the display of the RamaAnnotator model (e.g. via the ChimeraX Model Panel) temporarily turns off automatic validation, which will restart when display is turned back on.

__init__(atomic_structure, hide_favored=False, ignore_ribbon_hides=True)

Create the validator object, and add it as a child model to the target structure.

Args:
  • atomic_structure:

    • a ChimeraX.AtomicStructure instance

  • hide_favored:

    • if True, indicators will only appear for non-favored residues. (this can be changed at any time later)

  • ignore_ribbon_hides:

    • if True, the chimerax.HIDE_RIBBON bit will be ignored when deciding when to display a particular annotation. This is needed because the default ChimeraX ribbon representation hides the CA for any residue whose sidechain is un-displayed or missing (meaning that the glycine CA is always hidden).

property ca_radius

Sets the radius (in Angstroms) of the sphere overlaying each CA atom.

property color_scale

Returns a 3-tuple of (r,g,b,a) arrays defining the current colour scale.

delete()

Supported API. Delete this model.

property display

Show/hide the validation markup (automatic validation will pause while hidden).

property hide_favored

Show annotations for favoured rotamers, or just non-favoured/outliers?

pickable = False

Whether this drawing can be picked by View.picked_object().

static restore_snapshot(session, data)

Create object using snapshot data.

restrict_to_selected_residues(residues)

Restrict validation to a defined set of residues. Use track_whole_model = True to once again cover all residues.

Args:
  • residues:

    • A chimerax.Residues instance

take_snapshot(session, flags)

Return snapshot of current state of instance.

The semantics of the data is unknown to the caller. Returns None if should be skipped. The default implementation is for non-core classes and returns a copy of the instance dictionary (a deep copy of lists/dicts/etc., but shallow copy of named objects). Named objects are later converted to unique names.

property track_whole_model

Tell the validator to track/annotate all protein residues in the model (the default starting state).

RotamerAnnotator

class chimerax.isolde.validation.RotamerAnnotator(atomic_structure)

Handles the task of real-time validation of rotamers for a single chimerax.AtomicStructure and drawing of 3D indicators of their current scores. Designed to be mostly “fire-and-forget”:

ra = RotamerAnnotator(atomic_structure)

adds the :py:class`RotamerAnnotator` as a child model to atomic_structure and will update its validation drawing every time the coordinates change. Alternatively:

from chimerax.isolde import session_extensions as sx
ra = sx.get_rota_annotator(atomic_model)

creates the RotamerAnnotator if it doesn’t exist, or returns the existing one if it does.

Each rotamer score visualised as a 3D exclamation mark surrounded by a spiral, which changes colour and grows with outlier severity. By default only non-favoured rotamers are flagged.

Turning off the display of the RotamerAnnotator model (e.g. via the ChimeraX Model Panel) temporarily turns off automatic validation, which will restart when display is turned back on.

__init__(atomic_structure)

Create the validator object, and add it as a child model to the target structure.

Args:
  • atomic_structure:

    • a ChimeraX.AtomicStructure instance

property color_scale

Returns a 3-tuple of (r,g,b,a) arrays defining the current colour scale.

delete()

Supported API. Delete this model.

property display

Show/hide the validation markup (automatic validation will pause while hidden).

property hide_favored

Show annotations for favoured rotamers, or just non-favoured/outliers?

pickable = False

Whether this drawing can be picked by View.picked_object().

static restore_snapshot(session, data)

Create object using snapshot data.

restrict_to_selected_residues(residues)

Restrict validation to a defined set of residues. Use track_whole_model = True to once again cover all residues.

Args:
  • residues:

    • A chimerax.Residues instance

take_snapshot(session, flags)

Return snapshot of current state of instance.

The semantics of the data is unknown to the caller. Returns None if should be skipped. The default implementation is for non-core classes and returns a copy of the instance dictionary (a deep copy of lists/dicts/etc., but shallow copy of named objects). Named objects are later converted to unique names.

property track_whole_model

Tell the validator to track/annotate all rotameric residues in the model (the default starting state).