This thread is for questions about the new alignment tool. Any bug reports (or suggestions arising) should go in the feedback tracker.
The video shows comparing the protein being worked on with a template backbone.
Where does this template backbone come from? How do we use this in a regular puzzle, or is this just applicable to the Quest to Native where there is a guide (template?) to use?
Templates come from known proteins that are similar to the proteins we are trying to solve.
For example, in most of the mini-CASP puzzles, there hasn't been any templates for these soon to be solved proteins (which is one of the main reasons they are being solved), these are often called de-novo, ab-initio, or template-free targets.
In the CASP experiment, most of the targets are in the 'comparative modeling' or 'template based modeling' category. These are proteins where there is a similar structure that we can use as a starting point (but often there is still a lot of work to be done).
This is why we are very excited about the alignment tool, and why we want to give you a lot of practice with it before CASP 9 starts in May, because we believe that this will be a very powerful tool for you to use during CASP.
Here is more info about CASP 9 and templates: http://predictioncenter.org/casp9/index.cgi#scope
Look at puzzle 263: Alignment Freestyle. When puzzle at the beginning, all the segments are loops. After applying alignment tool, some segments become sheets or helices depending on known protein structure. This state is something like "starting point" for following playing. But some tools like "Local Wiggle" recipe reset all the segments to loops again, and protein seems like a mess without secondary structures. I think we need tool to save and restore secondary structures.
Yes, saving secondary structure is pretty highly voted in the feedback tracker so we are planning on adding that.