Ideal SS not making good helices on 879

Case number:845813-997530
Topic:Game: Tools
Opened by:Susume
Status:Open
Type:Bug
Opened on:Tuesday, April 22, 2014 - 03:00
Last modified:Wednesday, April 23, 2014 - 03:12

Ideal SS is making helices that are too stretched out lengthwise and don't have helix bonds. I had to use Idealize after Ideal SS to get the helices to shorten up and form bonds.

Shared with scientists "879 helices not ideal" showing the too-long helices made by Ideal SS.

(Tue, 04/22/2014 - 03:00  |  3 comments)


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

There is some confusion about what Idealize SS does - Idealize SS modifies standard backbone torsion angles, while regular Idealize modifies the inter-residue dofs. So if your inter-residue dofs are messed up, you still wont get a perfect helix.

I kept them separate because I figured this way gave you more control (you can always just run Idealize and Idealize SS), but I think it's worth just making Idealize SS also run an idealize for the sake of preventing confusion.

Angus's picture
User offline. Last seen 3 days 1 hour ago. Offline
Joined: 06/04/2008
Groups: Beta Folders

What is an "inter-residue dofs" ?

I don't believe I've seen that term before.

jflat06's picture
User offline. Last seen 6 days 8 hours ago. Offline
Joined: 09/29/2010
Groups: Window Group

DOF stands for degree of freedom. Things like how far apart two bonded atoms are, or the angle formed by 3 bonded atoms.

The degrees of freedom that connect two residues together aren't actually supposed to be "free" at all - they have very specific values, and straying away from those values results in unideality.

However, in practice, these values do vary, either inherently in structures (only slightly) or from being introduced by tools. For example, tools like the cut tool let you form very poor values for these DOFs, since you can rejoin the two residues at totally wacky lengths and angles.

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