helper_pdb2vol - PDB files to atom coord list and volume

version 1.0.8 (3 KB) by Carson Purnell
Generates a density volume from a PDB, and provides intermediate list of atom coordinates. Dramatically faster than pdbread.


Updated Wed, 29 Jun 2022 17:44:31 +0000

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This function was made to bypass the incredibly slow speed and significant limitations of matlab's pdbread function for the purpose of generating density maps of protein(s). It uses the most optimized text read functions available.
It is highly simplified and does not provide any pdb record information except a coordinate list from the atom records (not hetatm currently) and the element ID for those coordinates. The density map is output at a pixel resolution specified in angstroms, and stored in a cell array. For multi-model pdbs, each model is output separately into its own cell with the same bounding box, allowing the volumes to be easily summed or otherwise operated on.

Cite As

Carson Purnell (2022). helper_pdb2vol - PDB files to atom coord list and volume (, MATLAB Central File Exchange. Retrieved .

MATLAB Release Compatibility
Created with R2019b
Compatible with any release
Platform Compatibility
Windows macOS Linux

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