Questions tagged [pdb]

Protein Data Bank, a publically available database of molecular structures of proteins

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How to get a pdb file of a single atom?

I am trying to get a pdb file that contains a single atom, it doesn't matter if it's Hydrogen or another atom. How can I obtain this? Are there any pdb files with just a single atom available to ...
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How can I perform a 1:1 sequence-structure alignment for a pdb template dimer and homologous dimer sequence?

I have: 1. A PDB dimer protein structure template of a real solved protein. 2. An unsolved, but highly homologous dimer protein (>90% sequence identity.) How can I use MODELLER to make a theoretical ...
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How does RCSB determine the origin of the Cartesian coordinate system utilized in all PDB files

When perusing through the text version of a PDB file, I noticed in records that begin with "ATOM," there are x, y, and z coordinates for these atoms. How is the origin of each molecule's Cartesian ...
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How to convert PDB file of Amino Acids to rotamer tuples list of all AAs instances

Either by Python command, or via specific application (like Chimera) publicly available. Please provide example or link to one of. I have to detect AA location within MAP (density) 3D matrix. And to ...