"Alignment Editor" for "Alignment tool"

Case number:845813-989259
Topic:Game: Tools
Opened by:Rav3n_pl
Opened on:Saturday, February 12, 2011 - 15:29
Last modified:Wednesday, February 18, 2015 - 00:50

After hours fighting with last denovo puzzle some "simple" idea pops in: alignment editor.
We have pretty cool thing witch is alignment tool. But we can only use posted templates to thread (or mix parts from it) and we can use it only in selcted (dedicated) puzzles.

My idea is:
- set (guess or whatever) secondary structure
- copy that as straight sheets and ideal helices connected by elastic loops in "simple" 3d editor (just rotate view and drag/rotate/lock parts)
- move parts not watching at score, clashing etc - just make us align protein to shape we like to see
- optimize shape inside editor - make sheets parallel, all parts close to minimize voids (maybe some "glue" and minimum/optimal distance between elements)
- thread that shape

Also, loading current shape to editor should be possible to edit it quickly (ie move helix to other side).
I think some Bezier curves to form loops between structures and bend sheet/s can be used.

(Sat, 02/12/2011 - 15:29  |  9 comments)

beta_helix's picture
User offline. Last seen 2 weeks 4 hours ago. Offline
Joined: 05/09/2008
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changing assignment

Joined: 09/18/2009
Groups: SETI.Germany

Sounds very nice.

Joined: 08/09/2010
Groups: foldeRNA

I think it might also be useful to design this tool so it could be used between various solutions, so that even a shared solution could be used as an alignment. This would be useful in piecing together different regions from different solutions obtained through a group.

Joined: 09/18/2009
Groups: SETI.Germany

Yes, storing a solution or any other puzzle state and using it for alignment sounds very useful!

sgc9812's picture
User offline. Last seen 11 years 17 weeks ago. Offline
Joined: 04/07/2011
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I'd like to second the idea of an Alignment Editor...

What I find I need in the Alignment Tool is an accumulated template -- a "My Best Template" [MBT] field, into which I can accumulate and manipulate all my best ideas [from partials] in one place. I'd like to drag partials from active and reserved templates into MBT. After editing and aligning for a great score, only then do I want [or need] to Thread MBT.

As the tool currently operates, partials are committed to the active view, but there is no history or record of the alignment efforts. I lose track of portions I have previously threaded and those that still need attention.

[There may be an opportunity to refactor the Active Field so that it offers the functionality of the MBT field.]

[Apologies if this is already implemented somehow, or a poor suggestion -- I'm very much a newbie!]

infjamc's picture
User offline. Last seen 20 hours 49 min ago. Offline
Joined: 02/20/2009
Groups: Contenders

Re: sgc9812

You can approximate the MBT by saving a solution and then loading it as a guide (which will generate a temporary template called "GUIDE" in the Alignment Tool).

Joined: 06/17/2010

A bump.
We have now pretty big one 450 which can be edited much easier in way I suggest.
Work on it can look like this:
- we reset puzzle to one of star
- we fix secondary structure in way we see it is better (longer/shorter sheets/helices)
- we load it into alignment editor
- in editor we fix helices to perfect shape and align sheets in order (loops are ignored in this step)
- we "add" loops in shape we see best
- we thread created alignment
- we fix clashes etc....
- we own puzzle ;]

I that way we can produce much more different poses in much shorter time, ie after we stabilize we can see that sheets have to be reordered we load current pose in editor, move sheets and made partial thread only for that sheets and surrounding loops. Much faster than rebuilding or pulling them in new place.

Joined: 06/17/2010

A bump ;]
In new ugly looking ED puzzle it would be extremely useful to "draw a patch" in what we see in ED then thread it.
It can look as we see in threading tool - transparent current position/ED and colorful piece to bend and match. No score, no clashing, just bend it in place and thread.
Or make pieces: sheets, helices, then drag them into ED shadow, plot patch for loops and thread it.
Manual work on so distorted ED and messed puzzle is real pain... Working in way I describe would allow us make many more alignments than we can do using bands, dragging and manual rebuilds.

Joined: 06/17/2010
Status: Open » Closed

Closing. Cutting, idealize ss, move, etc. is already possible.


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