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jianlin-cheng / Cryo2Struct

Deep learning tools for converting cryo-EM density maps to protein structures
MIT License
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How to extract gold struct and visualize protein sequence? #3

Open LiuJoffrey opened 5 months ago

LiuJoffrey commented 5 months ago

I am trying to extract the gold struct from the pdb files. Where and how to read the protein sequence chain and compare it with the sequence struct predicted by the HMM?

nabingiri commented 5 months ago

Hello @LiuJoffrey, I am guessing that you want the carbon-alpha only structure extracted from .pdb files (protein structures). If thats the case, the script you are looking for is available here: https://github.com/BioinfoMachineLearning/cryo2struct/blob/main/preprocessing/get_ca_from_pdb.py

The protein structures can be visualized using UCSF Chimera (https://www.cgl.ucsf.edu/chimera/). Please download the tool and open the .pdb file with UCSF Chimera to visualize it.

To read the structures in Python program please use biopython package available here: https://biopython.org/.

We used multiple metric to compare the true protein structure that is deposited into Protein Data Bank and structure predicted by Cryo2Struct (more is available in results section of Cryo2Struct manuscript : https://doi.org/10.1101/2024.01.02.573943). Among them a widely used tool is : Phenix.chain_comparison tool available here: https://phenix-online.org/documentation/reference/chain_comparison.html . It can be run as : phenix.chain_comparison target.pdb query.pdb