Protein Folding Documentation - alan-turing-institute/protein_folding GitHub Wiki

This Page is a documentation on how to configure or modify the Protein Generator in Rhino Grasshopper

Key Functionalities

  • Visualise any PDB file and create interpolation between two states.
  • Create custom slices of chains of Amino Acids.
  • Visualise Heavy water data
  • Configure protein visualisations (2 LODs)
  • Mask slices based on AA order
  • UI

Main Set-Up structure

Protein Generator 3D is fully built in grasshopper, configured to instantiate protein structures from PDB data and link them to data deriving from the protein experiments with heavy water.
There are 3 main modules in Grasshopper:

  1. The PDB parser, which is used to parse and visualise the open PDB files
  2. The State Data parser, which is used to parse and visualise the State data deriving from the experiments
  3. and the UI module, which is creating the Grasshopper real-time Interface using the open source plug-in Human-UI.

diagram

Here is how the modules are structured inside the code editor in Grasshopper: 3 modlues

The first step is to input the path of the 2 PDB state files in the "Parse PDB" section (active and inactive). This can easily be done by double-clicking and editing the text box with the path module on the far left and input the right path to your files.

parse pdb

The second step is to input the path of the state data from the experiments in the "Parse State data" section. Similarly to before this be done by double-clicking and editing the text box with the path module on the far left and input the right path to your files.

parse data

Finally the last step is to activate the Interface of the app on the interface section on the top of the visual code by setting the toggle button into "True".

toggle

Advantages and Limitations of Rhino Grasshopper for this project

Advantages:

  1. One the most powerful 3D visualisation engines currently available. For images, animation, video and 3D interactive content.
  2. Its the top Parametric/Procedural 3D engine, community driven using the open source Grasshopper engine for the generation of 3D content using simple visual language and with great documentation.
  3. Python Integration.
  4. Available open source, ready-made modules for 3D visualisation and libraries for scientific visualisation of proteins (Alba).
  5. Customisable open source UI engine (Human UI).
  6. Tool to create quick sketches of interactive 3D content.

Limitations:

  1. Though Grasshopper is free and open source, Rhino is not freely available. (free for academics upon request)
  2. Not stand-alone, requires installation of Rhino 3D, though there are available free online viewers to run grasshopper scripts.
  3. Version control may be tricky to standardise.
  4. Human UI is not currently available for Mac users.