Chen Sun

Chen Sun

she/her

Structural Biologist | Cryo-EM | Cryo-ET | Cell Therapy & Drug Discovery | Deciphering molecular structures to drive therapeutic innovation

Blog posts

2026

Ctffind3

less than 1 minute read

Published:

Run CTFFIND3 with Multiple CPUs

2025

Centrifugation Types and Tips

3 minute read

Published:

There are two main types of centrifugation: differential centrifugation and density gradient centrifugation. Differential pelleting is commonly used to pellet cells, bacteria, and other large particles based on differences in mass, density and shape.

Aquilos Cryo-FIB milling protocol

3 minute read

Published:

Step 1: Initial Setup

  • Write down chamber pressure.
  • Fill liquid nitrogen to the tank.
  • Cool down the heat exchanger.
  • Set Nâ‚‚ gas flow rate to 180 mg/s.

2023

How to run relion on Herman cluster?

1 minute read

Published:

I’m sharing a SLURM submission script that’s tailored for running RELION on Herman cluster. While an interactive session can be helpful for initial testing, debugging, and code troubleshooting, it’s recommended to utilize the full potential of the cluster by submitting jobs through the SLURM system using the sbatch command.

2019

What Does Fourier Transform Do to Cryo-EM Images?

1 minute read

Published:

Cryo-EM images are formed by pixels with different intensity in grayscale. Each pixel is represented as a number in the image file. Below is a table simulating the pixel intensity of an image.

Amyloid processing tips

2 minute read

Published:

  1. Amyloid Atlas https://people.mbi.ucla.edu/sawaya/amyloidatlas/

Good box size for image processing

1 minute read

Published:

Criteria for good image size:

  1. even number (and divisible by 4)
  2. largest prime number factor is small (<=7) to make FFT faster
    List of good numbers (<=2000):
    All: [16, 20, 24, 28, 32, 36, 40, 48, 56, 60, 64, 72, 80, 84, 96, 100, 108, 112, 120, 128, 140, 144, 160, 168, 180, 192, 196, 200, 216, 224, 240, 252, 256, 280, 288, 300, 320, 324, 336, 360, 384, 392, 400, 420, 432, 448, 480, 500, 504, 512, 540, 560, 576, 588, 600, 640, 648, 672, 700, 720, 756, 768, 784, 800, 840, 864, 896, 900, 960, 972, 980, 1000, 1008, 1024, 1080, 1120, 1152, 1176, 1200, 1260, 1280, 1296, 1344, 1372, 1400, 1440, 1500, 1512, 1536, 1568, 1600, 1620, 1680, 1728, 1764, 1792, 1800, 1920, 1944, 1960, 2000]
    2: [16, 32, 64, 128, 256, 512, 1024]
    3: [24, 36, 48, 72, 96, 108, 144, 192, 216, 288, 324, 384, 432, 576, 648, 768, 864, 972, 1152, 1296, 1536, 1728, 1944]
    5: [20, 40, 60, 80, 100, 120, 160, 180, 200, 240, 300, 320, 360, 400, 480, 500, 540, 600, 640, 720, 800, 900, 960, 1000, 1080, 1200, 1280, 1440, 1500, 1600, 1620, 1800, 1920, 2000]
    7: [28, 56, 84, 112, 140, 168, 196, 224, 252, 280, 336, 392, 420, 448, 504, 560, 588, 672, 700, 756, 784, 840, 896, 980, 1008, 1120, 1176, 1260, 1344, 1372, 1400, 1512, 1568, 1680, 1764, 1792, 1960]

What is the Preferred Orientation Problem?

2 minute read

Published:

Preferred orientation occurs when most of the particles present the same view in the EM image. This has been a persistent issue for high-resolution structure determination with cryo-EM, especially for asymmetric samples. It is typically caused by the adherence of the sample to the air-water interface or to the substrate of the grid (e.g., carbon film or graphene oxide).