Tutorial 6-3 Aligning Sequences

Case number:954892-991750
Topic:Developer Preview
Opened by:mimi
Opened on:Saturday, February 4, 2012 - 19:52
Last modified:Monday, February 6, 2012 - 23:30

On the new tutorial the instruction "Good, now SHAKE and WIGGLE to finish"
appears immediately the alignment has been threaded and the cut appears.

This is misleading because you need to do three other things BEFORE using Shake and Wiggle

- Close the Alignment Tool
- Use the Move tool to reposition the protein
- Click on the cut

It would be good to have instructions to say that these need to be done
and to delay the appearance of the "Shake and Wiggle" instruction
until after the cut has been clicked on.

If you shake and wiggle BEFORE clicking on the cut
then no points are registered although floaters appear to say that you are gaining points

(Sat, 02/04/2012 - 19:52  |  4 comments)

beta_helix's picture
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Thanks for pointing this out, assigning...

jflat06's picture
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This is actually intentional, as generally shaking and wiggling BEFORE closing the cut will yield better results.

mimi's picture
User offline. Last seen 1 year 51 weeks ago. Offline
Joined: 11/17/2008
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The problem is that no points are registered before you click on the cut.
So that it appears as though it isn't working.
Can they be made to show?

It would still be good to include an instruction to close the alignment tool
and use the Move tool
before the shake and wiggle box appears

Susume's picture
User offline. Last seen 1 day 12 hours ago. Offline
Joined: 10/02/2011

Even if you click on the cut and successfully close it, no points register from shake and wiggle, unless you have wiggled before closing the cut. Once you reach this point, there is apparently no way to recover except to reset the puzzle. If you want to emphasize that one should wiggle before closing the cut, perhaps that wiggle deserves to be the final item in a help bubble, and closing the cut can begin the next help bubble.

My teammate gmn reports that he was able to complete the tutorial without moving any aas in the alignment tool at all.


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, RosettaCommons