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

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My Python Code for Various Molecular Structure Visualization and Analysis Tasks

• SPARTAN_FIXER
  • a python 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.
• 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 [here http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Split_NMR-style_multiple_model_pdb_files_into_individual_models ]
• Wayne Decatur's Python Scripts for Molecular Structure Analysis

Webserver

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

Code

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