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!