Get distances between atoms with Bio.PDB
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6.8 years ago

Hello everyone,

I'm trying to get the distances between the atoms of two different chains of the same pdb file.

I'm using python and my goal is to do that with a lot of pdb files with more than two chains that i have.

I only want the distance between pairs of chains.

 

Thanks

Python Biopython Bio.PDB Protein interaction • 4.2k views
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6.8 years ago
Peter 6.0k

This is old now, but here's how I did something similar about 10 years ago: http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/protein_contact_map/

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I have tried this one but seems to have some problems with the files with Hetero atoms

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Perhaps ask a more detailed question about hetero atoms, I would suggest signing up and using the biopython mailing list for this: http://biopython.org/wiki/Mailing_lists

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