New Visualization Options
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 105 1129 | Thu, 07/18/2013 - 22:19 | 4 comments )