User:Wayne Decatur/Code for Molecular Structure and Visualization Work

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My Python Code for Various Molecular Structure Visualization and Analysis TasksMy Python Code for Various Molecular Structure Visualization and Analysis Tasks

  • SPARTAN_FIXER
    • a Python (2.x) program that fixes Spartan'08 output files in so-called PDB format, converting them to be true PDB format. The fixed files can then easily be used in Jmol.
    • A webserver version of this is is running here. You can enter your data and have it analyzed without needing to download anything.
  • Wayne Decatur's Python Scripts for Molecular Structure Analysis
    • multiple_model_PDB_file_splitter.py
      • It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
      • You specify the structure file when you call the program.
      • Written in Python 2.x.
    • super_basic_multiple_model_PDB_file_splitter.py
      • A very basic multiple model PDB file splitting script written in Python 2.x.
      • It takes a multiple model PDB file and splits up the models to produce as output each of the models as a separate PDB file.
      • This basic version requires you to paste the complete PDB file text into the script before you run it. I put this out here in case it helps anyone understand what is going on; it was inspired by code at here
    • merge_multi_PDBs_into_single_file.py
      • A script written in Python 2.x to merge multiple PDB files as individual models in a single PDB file. The individual models are placed in a single folder..
      • It has advanced options that let you control the order of the individual models or control the starting numbering for the first model.
    • And more available here, with several of them demonstrated actively in Jupyter notebooks by launching 'binder' sessions from .here.
  • In addition to my Python Scripts for Molecular Structure Analysis, my pymol-binder adds some of my own code in for handling structures via PyMOL.

Webserver for Python codeWebserver for Python code

  • Much of the more involved code featured for Spartan_Fixer is running in a webserver form here. You can enter your data and have it analyzed without needing to download anything.

Obtaining the Python CodeObtaining the Python Code

See here for getting my code in a form you can use on your machine or that you can modify.


DockerfilesDockerfiles

  • Dockerfile to build images that will compile CNSsolve 1.21. A modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication here.
  • Dockerfile for a modified version of CNS to run the scripts for XL-MS Protein assembly, that software is referred to as XL-MOD in the publication here.

Related Python resources by othersRelated Python resources by others

  • atomium is a Python library for opening and saving .pdb, .cif and .xyz files, and presenting and manipulating the information contained within. Documentation is at https://atomium.samireland.com/ .
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