qiskit-xyz2pdb

This program is designed primarily to convert XYZ files from the results of Qiskit's protein folding algorithm, but may also work with other similar XYZ files for protein coordinates. There are two options for the output: 1) a hetero atom (HETATM) format with connect records (CONECT), and 2) a conventional alpha carbon trace protein pdb format. In both outputs, each set of coordinates corresponds to the alpha carbon of each residue in the sequence.

Install

The qiskit-xyz2pdb package is available on the Python Package Index and Conda and can be installed with the following command line:

# Install the package through PyPI
$ pip install qiskit-xyz2pdb

# Install the package through the Conda package manage
$ conda install qiskit-xyz2pdb

Features

The hetero atom format is most useful for quick visualization, using a program such as NGL viewer. Note: this option assumes that the XYZ coordinates are all consecutively bound forming a continous single chain; it assumes that there are no side chains, and the CONECT records reflect this. How to run with this option:

$ qiskit-xyz2pdb --in-xyz inputfile.xyz --out-pdb outputfile.pdb --hetero-atoms

The conventional alpha carbon trace format is more versatile and can be used for further research beyond visualization - such as reconstructing the full backbone and sidechains, adding a force field, and then performing molecular dynamics simulations. How to run with this option:

$ qiskit-xyz2pdb --in-xyz inputfile.xyz --out-pdb outputfile.pdb --alpha-c-traces