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Transform Molecules

Translation of Molecules

API: translate_molecules

GUI: Molecules > Translate molecules

Translation is a transformation of positional coordinates without changing the orientation of the molecules. There are two types of translations.

  1. Internal translation: The shifts \((dz, dy, dx)\) are applied to the internal coordinates. For example, internal translation \((1, 0, 0)\) of tubulin molecules results in a microtubule with larger radius.
  2. External translation: The shifts \((dz, dy, dx)\) are applied to the external (world) coordinates. For example, external translation \((1, 0, 0)\) of tubulin molecules results in a microtubule that is shifted along the \(z\)-axis of the tomogram.
Kinesin binding sites

Following code prepares molecules for the kinesin binding sites, given a molecules layer named "Mole-0" is correctly initialized at the tubulin positions.

ui.sta.seam_search_manually(layer='Mole-0', location=0)
ui.filter_molecules(layer='Mole-0', predicate='col("isotype-id") == 0')
ui.translate_molecules(layers=['Mole-0-Filt'], translation=(2.0, 2.04, 0.0), internal=True)

Rotation of Molecules

API: rotate_molecules

GUI: Molecules > Rotate molecules

Rotation is a transformation of the orientation of the molecules without changing the positional coordinates. Only internal rotation is implemented now.