3/18-3/25/2017: Week 6- Combining the Molecular Modelling Softwares' Benefits into a Powerful, Revised Foldit

So this week, I took some time to confirm my research into each of the three 3D modelling softwares which I have been using for molecular and protein modelling. Afterwards, I grouped the benefits of each program so that I might better lay out a road map which the Rosetta Commons may follow to modify their Foldit product so that it may be more multifaceted and applicable to a wider variety of circumstances.

Additionally, I considered some other features which I'd add given the release of the Foldit source code.

Foldit base

•3D modelling

•Default ribbon structures

•Solid molecular shapes (smallest manipulable units are amino polymer side chains)

•Collision-elimination algorithms

•Hydrophobic/hydrophilic molecules are labled

•Hydrogen bones are illustrated and their importance to protein synthesis is aptly demonstrated

Introductory protein design features

Avogadro

•Molecule construction

•Import functionality

•Range of modelling goes from atoms to full-scale molecules

•Automatic geometry correction algorithms

•Detailed imaging

•Implement the range of modelling to include Foldit ribbon structures and Avogadro ball-and-stick model via simple if statement.

PyMol

•Command line features with easy access to computer files

•Replace tool bar in Foldit

•Frame –by-frame move/playback feature and snapshot command

•Leave the UI in favor of a more aesthetically appealing one such as Avogadro or Foldit

•Combine the ideas of automatic molecule to atom viewing originating from Avogadro via simple magnification threshold addition and resulting shape change to PyMol’s Python code.

Additional features which may be added

•Pre-constructed cellular structures, such as ribosomes, with automatic re-focus feature. Since the programs deal with molecular and protein design, inserting a body hundreds of times larger than an amino acid would make the model unmanageable without auxiliary functions which automatically adjust the magnification and label all structures smaller than a few nanometers.

•An auto-play feature in which the interactions between two selected structures may be demonstrated. For example, if an amino acid chain and a ribosome are selected, the ribosome constructs a protein by accessing an online library via looking up the amino acid chain that’s entered into the ribosome. Thus, the process of protein synthesis may be illustrated with great detail. However, this would take a great deal of time and coding which may only be made available should the Rosetta commons allow access to the Foldit source code.

3/03-3/11/2017: Week 4 – Studying the Full Capabilities of Multiple Molecular Modelling Softwares

This past week has been very useful in terms of gaining knowledge on the workings of the PyMol and Avogadro programs. Unfortunately, I would only be able to share this information with you through an absurd amount of function definitions and pictures, which I shall not bore you with.

However, there are two features which I am particularly excited about. One is the molecular geometry optimization function of Avogadro. In manually building or even editing uploaded molecules via the UI, it’s possible to utilize the Optimize feature so that the molecular geometry is corrected to reflect the laws of chemistry. This feature touches every aspect of the molecule short of its atomic pairings.

The second feature which I found is PyMol’s “movie” feature. This part of the program allows for an addendum to the load command which gives the option for multiple files to be loaded in reference to one another as different frames of a single “movie” or animation. By the syntax of load [file directory-specific name], [selection name], [state or “frame”].

Additionally, this week I found that both Avogadro and PyMol are both capable of loading .pdb files. This revelation makes a batch script I’d developed specifically for the purpose of automating the transferring Avogadro-created files to the PyMol environment totally useless. On the bright side, I got to study batch some amount and that was a rather entertaining adventure in itself.

This current week, I am beginning to work on my own archetype for the Foldit module by describing the functionalities I envision would be included in it as well as illustrating the sorts of coding methods I see being implemented to expand the platform’ uses.

See you next week!

2/20-3/03/2017: Weeks 2 & 3 – Understanding 3D Molecular Modelling

Since my initial post and abstract about my project, some changes have arisen. Firstly, rather than actually editing the source code of Foldit, I will be instead constructing an archetype for any future versions. This change was brought about by issues in obtaining access to the source code from the IP license holders, the Rosetta Commons.

Instead of straightforwardly working with Foldit, I will be using to other programs, PyMol and Avogadro, to design a system akin to what I’d like to add to Foldit. Avogadro is an advanced molecule editor and visualizer with very high processing capabilities. PyMol is an older software which depends on the Python language for its structure and functions. This feature allows it to have a command system based around the language. However, the learning curve for this command system is fairly steep and the user interface is nowhere nearly as intuitive as that of Avogadro’s.

The results of me attempting to better understand Avogadro (right) and PyMol (left) by inserting similar atoms/molecules in either program.

I still have much to learn about PyMol and Avogadro but I have been making steady progress with both programs. Next week I plan to utilize the knowledge I am continuing to gain in these programs to begin developing ways to take advantage of the respective benefits of PyMol and Avogadro.

At the moment, I envision this combined system to work by the initial molecules being constructed in Avogadro with its relatively simple building mechanisms, after which the molecules would be saved as perhaps .xyz files and thereafter loaded into PyMol. The purpose of .xyz files is to contain the x, y, and z coordinates of the data contained within the file. This extension is perfect for 3D modelling. Upon importing the file into PyMol, the file will be converted as need be to fit PyMol’s specifications and thus the molecule will be open to edits by manual interactions and commands in the UI. The specific features of this process is what I'll be working on now.

See you next time!