direct manipulation of the Nitrogen in the backbone

Case number:845813-989169
Topic:Game: Tools
Opened by:anthion
Status:Open
Type:Suggestion
Opened on:Wednesday, January 19, 2011 - 16:48
Last modified:Wednesday, April 20, 2011 - 22:15

Currently we can manipulate the positions of the C in the backbone and all the various atoms in the side chains. It seems to me that if we could pull on the N in the backbone we would be more able to directly influence the backbone score. The only way to influence the position of the N in the backbone is with the Rebuild tool which is rather random or by manipulating other backbone segments and hoping the N gets into a desirable position.
It seems a shame to leave this part of scoring to such a random or difficult process.

In short, please can we pull on the N atom in the backbone?

Anthion

(Wed, 01/19/2011 - 16:48  |  4 comments)


anthion's picture
User offline. Last seen 13 hours 9 min ago. Offline
Joined: 08/05/2010
Groups: Gargleblasters

I'm afraid I was confused and I mean to say pulling on the Oxygen atom. But I think being able to grab the N or the O would provide similar results. peptide bond: the peptide bond showing the N (blue) and the O (red)peptide bond: the peptide bond showing the N (blue) and the O (red)

Joined: 08/24/2010

Yes, here's an example from a recent puzzles

Take notice of the bent sheet, from Cartoon Thin View
Cartoon Thin View: Notice how the sheet residue is twistedCartoon Thin View: Notice how the sheet residue is twisted

Stick view + PolarH
Stick + PolarH view: Here's is whats actually happening, with respect to the N-terminus ( Blue atom )Stick + PolarH view: Here's is whats actually happening, with respect to the N-terminus ( Blue atom )

Joined: 06/17/2010

A bump. "Manual rebuild tool" is a great idea imo :)
Behavior of "normal" rebuild is totally random and we can`t force it to do what we want.

infjamc's picture
User offline. Last seen 2 years 37 weeks ago. Offline
Joined: 02/20/2009
Groups: Contenders

Until this proposed feature is implemented, you can try the following as a possible workaround in the meantime:

1. Go into full-atom mode.
2. Freeze everything except for the residue you want to work on and its two neighboring residues.
3. Place a rubber band on the backbone atom(s) you want to tweak. Typically, at least two bands are required, one to pull the atom in question toward the direction you want and another to pull a neighboring atom in the opposite direction.
4. Use a recipe to set the band strength to 10.
5. Wiggle, local wiggle, or rebuild.

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