3D variability error v2.11.0

3D Variability Analysis
1

Hello,
Thank you for the answer from last time.

This time, we updated the Cryosparc to v2.11.0.
I am trying to sorte out which particles are in which states, so i run a 3D Var Display job and choose cluster to get the particule coordinates.

Here is the error messages in below:
44

2

Hi @chengjinzhu,

Unfortunately the advanced modes in 3D var are not yet deployed in v2.11 but we have accidentally removed the assertion check that indicates this to the user… so you see an error message like the above. We are working to deploy the new functionality asap.

You can, for now, look at the .cs files themselves that are outputted from 3D variability to see the particle reaction coordinates. To open the .cs file, you can use numpy in python:

import numpy as n
data = n.load('path/to/cs/file')
data['component_0/value'] # this will be all the reaction coordinates of the particles along component 0

You can also use the new import functionality (https://cryosparc.com/docs/tutorials/data-management/#faq-cs-csg) to create a copy and modify the .cs file to select particles only with certain reaction coordinates. You can create the new cs files directly from python also:

with open(path, 'wb') as file:
    n.save(file, newdata, allow_pickle=False) # newdata is a modified or subset of the loaded data from the cs file

hope this helps for now! we will be releasing a simple API interface for dealing with .cs files more easily.

2 Likes