The Idealize Tool
I'd like to introduce a new tool that is coming to the Foldit client: The Idealize tool.
So what does this tool do? Well, proteins, there are certain degrees of freedom that can change (like the angle of a sidechain coming off the backbone), and some that really shouldn't (like the distance between two residues). You can see some examples of degrees of freedom which should not change here:
(credit The Rockafeller University)
You'll notice there are very specific values drawn into this picture that describe certain angles and distances between atoms. These values are called 'ideal' values, and in real proteins, their values do not change much.
In Foldit, sometimes these values start to get away from their ideal values, and you'll see this as a poor backbone score on a segment or two. These issues can be very hard to fix. The easiest way to introduce this problem is with cuts - if you make a cut and then try and close it at an odd angle, often times it will be quite difficult to massage out the problem.
With that, we've created the Idealize tool. This tool lets you simply set all of these degrees of freedom to their ideal values for a portion of the backbone. The tool works in the Classic interface via the right click menu, and will pop up in the selection interface when you have several residues selected. It is also available in the scripting interface with a call to IdealizeSelected().
For an example of where this tool can be used, look at the backbone below:
You may or may not be able to tell, but there are problems with this backbone. You can see what the backbone *should* look like in the following picture:
You can see that the blue portion should have a nice angle around 120 degrees or so. In the backbone on the top, however, it is near 180 degrees. This will result in a very poor backbone score in Foldit, and is something you want to fix.
And with the idealize tool, you can do just that! In the classic interface, right click the backbone where the issue exists, and select Idealize.
This will set the problematic degrees of freedom to their ideal values, and will make the backbone look like the second, correct picture. Note that while this tool only modifies values in the region you're working on, the changes cause one entire side of the protein to swing into a new position.
We hope this tool will be useful, and are happy to receive any feedback you have!( Posted by jflat06 105 1029 | Wed, 06/19/2013 - 00:19 | 7 comments )