Jayden

Intro#

Building a model for a huge cryo-EM map may be annoying, especially when it's supercomplex.

But now you can use ModelAngleo to build models for a cryo-EM map locally, without worry about data leakage.

Usage#

1. Ensure you have met the computing requirements of ModelAngelo: mainly GPUs with at least 8GB of memory.

2. Install

   1. Install Miniconda: https://docs.anaconda.com/free/miniconda

   2. Clone the repo and run the script:

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      git clone https://github.com/3dem/model-angelo.git
      cd model-angelo && source install_script.sh
      

3. Process:

   1. Before the start, you need to activate the environment by running conda activate model_angelo in the terminal.

   2. Building a map with FASTA sequence:

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      model_angelo build -v map.mrc -pf prot.fasta -df dna.fasta -rf rna.fasta -o output
      
      -v: map, in mrc format
      -pf: protein sequence
      -df: dna sequence
      -rf: rna sequence
      -o: output directory
      

      [!IMPORTANT]

      You don't need to repeat the sequence of a dimer in the FASTA file.

   3. Building a map with no FASTA sequence:

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      model_angelo build_no_seq -v map.mrc -o output
      

[!NOTE]

If the result looks terrible with unconnected chains, the map is probably in the wrong hand, just flip the map and run again.

Reference#

1. Article: https://www.nature.com/articles/s41586-024-07215-4
2. Code: https://github.com/3dem/model-angelo

此文由 Mix Space 同步更新至 xLog
原始链接为 https://xxu.do/posts/structure/Build-Models-for-cryo-EM-Maps-with-ModelAngelo