Rama dots in wrong position after inserting segments

Case number:699969-2002397
Opened by:Susume
Opened on:Sunday, May 1, 2016 - 23:10
Last modified:Monday, May 2, 2016 - 23:51

See shared solution "1226 rama dots wrong after inserting" on puzzle 1226. The rama dots for 3 residues are in the wrong place after I inserted other residues.

I inserted 4 residues into a helix (three became residues 24, 25, 26 and one became residue 41), which moved the loops on either end of the helix (they had been parallel to, and the same shape as, the loops on the other helix). Then I used Ideal SS on the newly elongated helix. Then I attempted to copy the loop at 69-71 onto the loop at 42-44, by dragging the dots for 42-44 on top of the dots for 69-71 (my 2nd video shows how it's supposed to work). Even though I made the dots match, the shape of the loop in the protein does not match. The thumbnail above the rama map shows each of the residues (42, 43, 44) having a different shape than its model residue (69, 70, 71), even though the dots are the same. Having identical dots should mean having identical shapes. Loop 42-44 and helix 24-41 should be roughly parallel to loop 69-71 and helix 55-68 in the protein, and their shapes in the thumbnail should be identical.

(Sun, 05/01/2016 - 23:10  |  2 comments)

Susume's picture
User offline. Last seen 1 day 18 hours ago. Offline
Joined: 10/02/2011

An easier way to see what's wrong is to change residues 42-44 in that share to sheet and use Ideal SS on them. You can see that they change to ideal sheet shape in the protein, but their dots are all over the map, rather than all being on top of the ideal sheet dots.

bkoep's picture
User offline. Last seen 1 hour 1 min ago. Offline
Joined: 11/15/2012
Groups: Foldit Staff
Type: Suggestion » Bug

Thanks for sharing, Susume. It looks like those residues have the correct φ and ψ torsions, but there is some very bad geometry at the peptide bond, which is why they have a strange conformation (you probably noticed those residues have a really bad Ideality score, too).

Normally, the solution for this would be to use the "Idealize peptide bonds" tool to fix the geometry and improve the Ideality score. But the tool doesn't seem to be working for me, and that's a problem. I'll have to dig into this a little more, sorry!


Developed by: UW Center for Game Science, UW Institute for Protein Design, Northeastern University, Vanderbilt University Meiler Lab, UC Davis
Supported by: DARPA, NSF, NIH, HHMI, Amazon, Microsoft, Adobe, Boehringer Ingelheim, RosettaCommons