New Visualization Options

Hey everyone!

We have some new visualization options coming to Foldit, and this post should give you a little information on what they are and how to use them.

The first two deal with the quality of the backbone angles:


Backbone connection Unideal - This warning will pop up when the connection between two residues in the chain is unideal. You can read more about unideality in this blog post: http://fold.it/portal/node/995357



Clicking on the warning will 'fix' the backbone by setting the distances and angles to their ideal values:




CIS peptide bond - CIS peptide bonds are when a normal peptide bond is 'flipped' 180 degrees, so that instead of zig-zagging back and forth like the backbone usually does, it makes a sharper turn. This type of bond is fairly rare in nature, and so it's often good to fix these up.



Clicking on the warning will 'fix' the backbone by converting the CIS peptide bond to a trans (normal) peptide bond.



These can be enabled/disabled via the "Show backbone issues" checkbox in the View tab.

The last new visualization option is the Electron Density Trim tool:


Electron Density Trim

This option is available in the Electron Density Panel. Trimming the density lets you only show the density that is 'close' to the current backbone. To use it, click the 'Trim Density' button.



This pops up a menu that lets you set a threshold from near to far of how far away you want to trim the density. If you're still trying to decide which bits of density to use, a far value might be better. If you're fairly sure you have the protein oriented well, then the near value might be best. In this case, I'm pretty sure I've got the protein fairly well placed, so I'll use a nearer value.



Clicking the Accept button will then trim the density to the selected value, leaving you with just the density around the protein. You can also click the cancel button to keep your current density.



Note that if you want to return to seeing all of the density, you can just set the trim value to Far and it will show everything.

We hope you find these tools useful, and your feedback on them would be greatly appreciated!

( Posted by  jflat06 123 1359  |  Thu, 07/18/2013 - 22:19  |  4 comments )
5
Angus's picture
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Confusion reigns!

Could you explain a little , or a lot more, about CIS vs. trans in the second version of the golden vanilla ice cream cone?

The popup just says "Cis backbone connection. Click to switch to trans."

Clicking just seems to pretty much explode the protein, not very useful.

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

Sure -

There is a degree of freedom between any two peptide bonded residues, the omega angle, which takes a value of either 0 degrees or 180 degrees.

Depending on the angle, the backbone either continues zig-zagging (like the bottom picture) or does a sort of hairpin (like the top picture).

The zig-zagging peptide bond is called 'trans' while the hairpin is called 'cis'.

We warn you about cis because, as it turns out, cis bonds are very rare in the natural proteins that we have observed (1000 to 1 in favor of trans).

There's a small exception to this in the case of prolines - when a proline is the top residue in a peptide bond, the ratio is about 3 to 1 in favor of trans, and consequently we do not create a warning about this.

Basically we are warning you because there is a statistically unlikely property of your protein.

As for the tool's usefulness - the main point of this change is to warn you about your cis bonds. What method you choose to employ to fix it is up to you. The tool provided isn't intended to flawlessly fix the problem every time, or else we would just do it automatically!

Joined: 09/21/2011
Groups: Void Crushers
About idealize

Question: how can the backbone score be still negative after idealize is done? Perfect angles, perfect distances, what is left that can cause negative scores?

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

The backbone score in the tab menu contains many different components, and not just the idealization.

Idealization only covers those degrees of freedom that are not supposed to change. There are many other forms of evaluating the quality of the backbone. One such evaluation uses Ramachandran plots: http://en.wikipedia.org/wiki/Ramachandran_plot

A Ramachandran plot shows the favored values of different (variable) backbone degrees of freedom for a particular amino acid type. We include the Ramachandran evaluation in the 'backbone' score category in the tab menu.

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