So, the where does the score on the Alignment Page fit in? If I try and get the highest score possible by moving the top chain around, I end up with large gaps, and moving the lower letters around doesn't help. So, how do I get a better match? By comparing versus the shadow of the original protein?
Hello GreatGreyhounds,
Unfortunately the alignment score is not perfect and is probably most useful for comparing different templates (to see which alignment to the query is giving you a better score).
The alignment score is based on BLOSUM (more info about that here if you are interested: http://en.wikipedia.org/wiki/BLOSUM) but basically what you are trying to is to minimize the number of gaps while trying maximize the alignment score.
In general, having 1 long gap is better than having a bunch of short gaps and this should be reflected in the score.
Definitely try comparing your threaded model to the native guide (once you've threaded it) and see if it seems closer to it than a different thread.
I hope you saw our new wiki page on the newest Alignment Tool:
First of all, make sure you have completed the following Intro Levels: 1-1 through 3-4 and 7-1 through 7-4, before trying to play this puzzle.
Once you have loaded this puzzle, click on "Show Alignment" to bring up the alignment tool.
This will bring up the sequence for the protein you are trying to solve (the letters on top) as well as the template sequence on the bottom (of a similar structure that you will thread your sequence onto).
You can move the letters around, trying to get rid of as many gaps as you can and maximizing the white blocks between the two sequences (which represents a good match).
Once you have an alignment that you like you can click on the SMILEY FACE to thread. This will take a while but if it is able to thread you will have a new structure to work on.
Make sure to click Align Guide (under Actions) after you have successfully threaded so that you can see how close you are to the native solution.
Also, once you have threaded successfully you will want to shake & wiggle sidechains (because you are threading your new sequence onto a protein that had different sidechains, so there will be many clashes) before you try to wiggle all.
If you are having trouble matching the native, you can learn some more expert tools in the following intro levels: 4-1 to 4-5.
Feel free to post any questions about this puzzle here in the puzzle comments!