Chen Sun

Chen Sun

she/her

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

Posts by Tags

Amyloid

Amyloid processing tips

2 minute read

Published:

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

Aquilos

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 N₂ gas flow rate to 180 mg/s.

AreTomo3

CLEM

ChimeraX

Cryo-EM

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.

EMAN2

FIB milling

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 N₂ gas flow rate to 180 mg/s.

FSC

Figure making

Filament

Amyloid processing tips

2 minute read

Published:

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

Fourier Transform

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.

GPU

HPC

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.

Leica

PhD

box size

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]

centrifugation

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.

command

commands

confidence interval

cryo-EM

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).

cryo-ET

error bar

fellowship

figure making

graduate school

graphene oxide grid

grid preparation

helical reconstruction

Amyloid processing tips

2 minute read

Published:

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

home-made grids

image processing

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.

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).

installation

outreach

postdoc

preferred orientation

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).

processing

protocol

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 N₂ gas flow rate to 180 mg/s.

purification

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.

relion

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.

sample

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.

science communication

script

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.

segmentation

sequence alignment

tomo

visualization