Alignment tool 'Cannot Thread', cutpoints, and memory effect

Case number:845813-992547
Topic:Game: Tools
Opened by:brow42
Status:Closed
Type:Bug
Opened on:Tuesday, May 1, 2012 - 14:37
Last modified:Wednesday, May 2, 2012 - 20:12

In the blog post for Apr. 30, I asked about the conditions for successful / failed thread. You can answer that here. But I'm really posting to point out that I've confirmed the memory effect! It's from the cutpoints.

On puzzle 550, pick 3kgrA and turn threading on. Then slide H 36 three slots to the right. The slide the other end of that block K 54, three slots to the left. Intuition says I'm back where I started but it has stopped threading. Even if I hit reset alignment, it won't thread! I think this has been causing a lot of my frustration.

The problem is that subsequence acquired a cutpoint when it first entered the gap at template V 31, and refused to thread after that. To make it align, I have to continue to my desired alignment, close cutpoints, and toggle threading on/off.

It looks like continuous threading is incompatible with the cutpoints. It was a neat idea. Before cutpoints, it would just resume threading whenever the alignment was acceptable. With cutpoints, threading has to be one-shot.

I would suggest a three-state threading button. Click to thread once (smileyface!) and then it turns off. Double-click to lock threading on. Click that to turn it off.

(Tue, 05/01/2012 - 14:37  |  5 comments)


beta_helix's picture
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Type: Suggestion » Bug

Thank you for posting a clear reproducible bug with the new alignment tool.
assiging...

jflat06's picture
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When I follow your instructions exactly, I am unable to get the alignment threading to fail. That said, I'm still able to get it into some weird state where the aligning will fail, but I'm not completely sure how it's happening.

I know that the alignment fails when the following occurs (R is a residue, - is a gap)

---RRR
RRR---

That is, the alignment will fail whenever there are adjacent gaps in the working protein and the template. This is a bug, and can be fixed.

But it seems that there is an additional case that is causing failure as well.

For a little clarification, your intuition on the first part - "On puzzle 550, pick 3kgrA and turn threading on. Then slide H 36 three slots to the right. The slide the other end of that block K 54, three slots to the left. Intuition says I'm back where I started but it has stopped threading." - Is incorrect. Moving H36 3 right and K54 3 left are not inverse operations. You cannot think of the template residue/gap sequence and the structure residue/gap sequence as independent. There is really only one thing - the alignment itself. And in terms of the alignment, when you move H36 to the right, it *would* create a gap in the top sequence. But a gap in both of the sequences does not make sense, and they cancel out.

jflat06's picture
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It would appear the other case is caused by alignments of the form

RRRRRR
RR--RR

When you shift the alignment, it only aligns every 3rd or so shift.

This and the other case are due to the way that the alignment handles gaps in the template. When there's a gap in the template, the tool *has* to put the residues in the game's protein *somewhere*. So what it does is it just attaches them on to the end of wherever the gap began. In the case I described before, the bug was that there wasn't a residue where the gap began, because there was a gap in the sequence. The second I'm not totally sure about, but it is almost certainly related as well.

brow42's picture
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I found the critical detail...I had the other two templates up, as well. This creates the gap at 31 that I mentioned.

I also found a new annoyance...the alignment tool copies the current selection (set either by a script or the selection interface). I can clear or change that selection in the alignment tool, but after any threading, it reloads that original selection! Very hard to move single residues when it keeps doing that.

screenshot of steps attached.

jflat06's picture
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Status: Open » Closed

This should all be fixed now, at least for the testing that I did. It should be in the next release.

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