The application is organized by themes that mirror the information available in the pdb101 web pages. The term "pdb" is short for Protein Data Base, a world wide collection of data on protein structure. The RCSB.org website hosts a US based collection of proteins and has links to other organizations worldwide.
Selecting a Molecule of the Month entry brings you into a detail view of the molecule highlighted. The "i" floating button will take you to the web page where Dr. Goodsell describes the significance of this molecule. The list of PDB entries further down the page gives the 4 letter names for the proteins referenced in the monthly highlight. If you select the "RCSB PDB" entry on the left - the application will open the PDB entry on the RCSB website.
If you select the graphic on the right, you can download the PDB entry from the website and explore it in a 3D viewer. From the 3D viewer you can:
- Rotate the model with one finger, or use two fingers to slide it around. You can also zoom in by squeezing your fingers together or zoom out by pushing them apart.
- You can go to the next PDB in the list by pressing "NEXT OBJ" or the previous one with "PREV OBJ".
- The "CHANGE VIEW" button will rotate your view through the "Ribbon", then "Ribbon+Stick" mode, followed by "Stick only", "Ball and Stick", and finally "Spheres". The "Spheres" model attempts to show the true relative sizes of the atoms in the protein.
There is still more work left to do on this application, so apologies in advance if you have any difficulties with it. One area that needs work is handling the viewing of hydrogen atoms - sometimes there are more in the model than can be shown on a battery powered device! Also the model is sometimes simplified to try to fit the view into memory. Some models are so large that only the "Ribbon" view can be shown.
The application content is downloaded from the wonderful
http://pdb101.rcsb.org web pages.
