Primary and Secondary Structures Generation

Goals:

The goal was to pick a molecule as our center piece for the fly-through as well as be the facilitator in generating file formats that were complaint with the needs of our group. There are several types of molecules but more important there are two main structures that lie within the molecule: primary and secondary. The generation of these structures was my primary responsibility as well as facilitate the isocontouring group.

Tools:

• RasMol http://www.umass.edu/microbio/rasmol/
• MolScript http://www.avatar.se/molscript/
• MidasPlus http://www.cgl.ucsf.edu/Outreach/midasplus/
• Ribbons http://sgce.cbse.uab.edu/ribbons/
• PyMol http://pymol.sourceforge.net/

All of these tools can be used to generate secondary structures. However, the difficulty aroused in file formats that Perfly could read. There were compliancy issues with reading VRML 2.0 files therefore we had to find a workaround this. Based on our pipeline of information, the molecular dynamics group would generate time-dependent PDB files. To generate IV files, the temporary only viable solution that Perfly can read, I used a tool called pdb2vrml.

Pdb2vrml seemed the best tool for what we were trying to achieve. At first the approach was to create geometry files, in our case VRML, which would ease the process in generating a scene using Cosmoworld. However there was some problems with Perfly reading VRML files but no problems with IV files so we had to figure out a work around to get IV files. The tools above generally outputted VRML files, however our approach changed and pdb2vrml make the tool at hand.

Generation of IV files:

1. pdb2vrml –ribbon –solid –pdb file.pdb file.iv <-secondary structure
2. pdb2vrml –pdb file.pdb file.iv <- primary structure

The explanation of the meaning of the molecules and the structures can be seen in the presentation: Primary/Secondary Structures.

Results:

• Created primary and secondary structures files for the anthrax toxin.
• 103 iv files for each frame within the trajectory for primary structure and secondary structure

What I have learned

• In order to fully gain the most out creating molecular objects, a clear understanding of the inner workings would be beneficial. A great deal of the beginning portion of the project was spent reading in understanding the chemistry and biology of molecules and proteins and understanding how the data can be represented.
• Tools are generally available out there on the internet that will ease the generation of files. The difficulty lies in taking these various tools and connecting them together to use them effectively to reach a final output.
• The visualization of molecules and proteins will prove to be beneficial in the biology world because it will provide a more clear model.
• The algorithm for generating the secondary structure of a protein is very trivial. Merely a sequence of parsing certain data from the PDB file and creating normals and using B-splines to connect the critical points together
• There are many tools that can generate static volumes of secondary structures but time-dependent tools are the more useful in terms of usefulness in the real world