Apo-CGRP

Dataset

Full Case Study

Part One: Setup

Ensure you have created a location to keep track of CryoSPARC projects:

Title Value
Title
Description Leave empty
Directory
Create Workspace Enable
Workspace Title Leave default

There are a few prepared jobs that we will import into the project. They were exported from a different CryoSPARC instance and transferred onto the local SSD of your EC2 instance.

  1. Navigate to the project directory:
  2. Make a new directory called imports and navigate into it:
  3. Move J188_nonuniform_refine_new
  4. Move J192_new_local_refine
  5. Move J719_volume_tools

Navigate to the workspace you just created, click on the dropdown next to 'New Job', select 'Import Job' and fill out the corresponding absolute path. Do this for all three jobs. You should see three completed jobs in the workspace:

Import Path Job Type Imported Job Title
Non-Uniform Refinement None
Local Refinement None
Volume Tools None

  • Input: particles from NU-refine job
  • Input: mask from imported Volume Tools job
Parameter Value
Filter resolution (A)
Cache particle images on SSD False

This job should take around 25 minutes to complete.

Create a 3D Variability Display job to visualize the results of the 3D Variability Analysis.

Parameter Value
Crop to size (after downsample)
Filter resolution (A)
Cache particle images on SSD False

This job should take around a minute to complete.

Download each component for both results and open them in UCSF ChimeraX.

Connect the volume from the imported Local Refinement job.

Use default parameters

The job should take ~4.5 minutes to complete.

Use the segger tool in ChimeraX to create a .seg file from the volume you just created. This will allow you to define the segments and connections for the 3D Flex job.

Segmentation in ChimeraX

Drag and drop the .seg file into the browser. Ensure the correct project is selected and click 'Upload'. Once complete you can copy the absolute path of the file to use in the next step.

Parameter Value
Segmentation file path
Segment connections
Base num. tetra cells
Min. rigidity weight
Mask dilation (A)
Mask threshold

The job should take ~10 seconds to complete.

Parameter Value
Number of latent dims
Rigidity (lambda)
Latent centering strength
Initialize latents from input True

Create a 3D Flex Generate job to visualize the results of the 3D Flex Training.

Input: results from 3D Flex Training job Input: volume from Non-Uniform Refinement job

Download the generated .mrc files and open them in UCSF ChimeraX.