3DVA Distribution Reaction Coordinate Plots

3D Variability Analysis
1

The distribution of reaction coordinate plots for my recent 3DVA jobs have been very high, which makes the interpretation of the produced plots hard.

When running 3DVA Display with Clusters, the plots are rescaled to exclude the extremes of the plot, but the Intermediate and Simple displays are not scaled, making it difficult to observe where the rolling window frames are located.

I thought perhaps changing the parameter “var_range_percentile” would help, but it doesn’t seem to have an effect on the Intermediate display type.

I am using quite a generous solvent mask for the 3DVA run, with a filter resolution of 6 Å. Not sure if that is contributing to the large spread of reaction coordinates? Any tips on how to reduce?

CryoSPARC Version: Master running v5.0.4, worker running v5.0.4

3DVA Reaction Coordinates

J540_result_components
J540_result_components1946×851 59.1 KB

3DVA Display Component 0, Clusters(5):

J549_histogram_with_clusters_in_selected_dimension
J549_histogram_with_clusters_in_selected_dimension1013×515 15.9 KB

3DVA Display Component 0, Intermediate(20):

J552_distribution_of_reaction_coordinates_mode_0
J552_distribution_of_reaction_coordinates_mode_0692×418 13.9 KB

2

Hi zahodnbd

Without further information I need to start by asking how clean is your dataset, and how many particles? Those plots are what I’d expect from interference of junk particles in the 3DVA algorithm, the best is if more experienced users or the CS crew could help here.