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741b: Blind Electron Density 9; Now with Templates!

Closed since about 9 years ago

Advanced Overall Prediction Electron Density


July 05, 2013
Max points

This Electron Density puzzle is a bit different because we have not trimmed the density. Again, the automated methods were unable to solve this structure using this huge density cloud. To make it easier for you, we are providing two different templates to start with. Use all your Electron Density & Alignment Tool folding skills to fit the density as well as you can and beat the automated methods! The secondary structure predictions have been loaded onto the starting model, with more details posted in the puzzle comments. NOTE: You will need to latest client to play this puzzle!

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beta_helix Staff Lv 1

The extended chain on 741 did not have the secondary structure predictions shown in the sequence logo below.

You will be able to load in your manual saves from 741 into this puzzle. If you did not manually save a solution in puzzle 741, you can go back to 741, manually save it, and the solution should appear in your manual saves for this puzzle, 741b.

Here is the original puzzle:

beta_helix Staff Lv 1

Here is the sequence logo predicted by the SAM server:

H = helix
E = sheet
C = loop (or coil)

The taller the letter at each position, the higher the probability of that specific secondary structure for that amino acid.

For example, the Valine at residue 107 is highly predicted to be part of a helix. However, the Valine at residue 137 is predicted to be in a sheet!

The above predictions are already on the starting model (based on the horizontal lines in the above figure).

Here are links to both templates in the PDB:

Cutaway view hint:
If you hover your mouse over a segment and type shift-Q, the game will hide parts of the protein and cloud that are not in the same plane as that segment - it cuts down on how much cloud you see at one time and makes it easier to focus. Q returns to normal view.

New Electron Density Features:

  • Notes can be added to the electron density if present. To add one, press TAB with the mouse over the density while the density panel is open. Use the recycle button in the note panel to erase one. (Note: saving and sharing these notes is a feature that should be in a future release)

The above video from our YouTube channel has Seth Cooper explaining how to add Notes to the electron density.

  • There is a button in the Electron Density Panel to focus rotation on the density. You can use the HOME or Q keys to refocus on the protein.
  • The density score of a residue may now be viewed in the tab menu

Because this is the first time we are combining Electron Density and the Alignment Tool, you'll notice that when you thread your sequence onto a template, it is nowhere near the density. If you want everything in the same place, after threading you can use the "Align Protein to Density" button in the Electron Density Panel and then press Q.