3DVA plot raw values

3D Variability Analysis
2

Hi @Eike ,

Glad that our 3DVA job is coming in handy! You can indeed extract and manipulate the raw data for each of the components. The raw data is found in the ‘{…}_particles.cs’ cryoSPARC file that’s located in the 3DVA job folder. You can import this file via a Dataset() object through our interactive Python shell (or a separate script/notebook) and then extract the reaction coordinates for each particle using the components_mode_X/value key. Here’s an example script that will extract two of the components as NumPy arrays, which you can then plot/export as necessary:

#Launch cryoSPARC’s interactive Python shell
cryosparcm icli

# … in the shell

#1. Import necessary modules
from cryosparc_compute import dataset

#2. Load particles
# Modify as necessary
cs_file_path = ‘./P167/J42/cryosparc_P167_J42_particles.cs’ 
particle_dataset = dataset.Dataset()
particle_dataset.from_file(cs_file_path)

#3. Extract components
c0 = particle_dataset.data['components_mode_0/value']  #(N,) numpy array
c1 = particle_dataset.data['components_mode_1/value']  #(N,) numpy array
#… etc.

You can find more information about .cs files in our ‘Manipulating .cs Files’ tutorial.

Hope that helps!
Valentin

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