621: Electron Density Puzzle

Case number:845813-993364
Topic:Game: Tools
Opened by:stg123123
Opened on:Tuesday, August 21, 2012 - 14:59
Last modified:Thursday, August 23, 2012 - 20:00

621: Electron Density Puzzle

If I change the threshold for the ED than my scor change as well. Also if I align the protein to the density I get some 100s points less.

I have now a solution far away from good but scores over 9000 points. If I aglin I get around 3000 points.

I use the main version.

Ciao STG

(Tue, 08/21/2012 - 14:59  |  6 comments)

jflat06's picture
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Joined: 09/29/2010
Groups: Window Group

Changing the threshold should not change your score. I am unable to reproduce this on the main client. What version of the game are you running? (You should be able to find it in General Options under Build ID).

Aligning the protein will often score less because the program uses and algorithm to align the protein that doesn't always work well.

Can you post a screenshot of your solution? It makes sense that your solution might look bad, but score well, because we are using a higher weighting on the fit for electron density for this puzzle. This means that you'll be rewarded for fitting the density much more than usual.

Joined: 10/11/2011
Groups: Beta Folders

If you align the puzzle with max threshold and than change threshold to minimum and align again, my score change by several 100s of points.

Joined: 10/11/2011
Groups: Beta Folders

The threshold I have to test again. I use 2012-07-24-50077M-win_x86

I attach the screenshot. So you see my best solution.

Joined: 10/11/2011
Groups: Beta Folders

And the file

marie_s's picture
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Joined: 05/18/2008
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I lost around 1000 points with alignement.
regain a little with wiggle.

brow42's picture
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Joined: 09/19/2011
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Facts about ED:

Part of your score is computed from how well your protein matches the entire cloud, visible OR invisible.

Threshold changes what is visible, but not your score.

Coarse alignment is to what is VISIBLE. It's always been this way. Probably on purpose. I suggest moving the slider to max visible before pushing the align button.

Coarse alignment doesn't work well unless you are already mostly the correct shape. It doesn't work AT ALL if your protein cannot be frozen as a single continuous peptide (2 or more pieces, uncertain about the effect of cuts).

Quote from jflat06: "I should just remove that button."


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
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