Restricted Mesh Annealing (RMA)

Restricted Mesh Annealing (RMA) is a constrained subtomogram alignment algorithm that was introduced in our work. It imposes longitudinal and lateral constraints between molecules and optimize the alignment score using simulated annealing.

As an example of using RMA, see the case study.

Run RMA on a Landscape

API: run_rma_on_landscape

GUI: Subtomogram Averaging > Landscape > Run annealing (RMA)

List of Parameters

1. Select the landscape in the "landscape layer" combobox.
2. "Longitudinal range (nm)" is the constrant of the longitudinal distance between neighboring molecules.
3. "Lateral range (nm)" is the constrant of the lateral distance between neighboring molecules.
4. "Maximum angle (deg)" is the another constraint. It is the maximum allowed angle between the spline tangent and the vector connecting the two molecules.
5. "temperature time const" is the time constant of the simulated annealing. Larger value means slower annealing. 1.0 is usually a good value.
6. "random seeds" is the seed values for the random number generator. The "Add" button will randomly add a new seed value.
7. You can preview the distribution of the longitudinal/lateral distances by clicking the "Preview molecule network" button.

Run RMA without Constructing a Landscape

API: align_all_rma

GUI: Subtomogram Averaging > Alignment > Simulated Annealing