Partial alignment-- first thoughts
|Opened on:||Thursday, May 13, 2010 - 04:22|
|Last modified:||Friday, April 20, 2012 - 22:28|
First of all, thanks for implementing this tool. However, trying it in real puzzles revealed that using it in practice is more difficult than expected for several reasons:
1. Right now, there is still no way to align the entire protein in one go by selecting pieces from the different templates.
2. When doing a partial alignment, the rest of the protein is fixed. This could be problematic when threading across different templates, as their backbone locations could be very different.
A good example of this is #305. For a good overall alignment, the template with a score of 343 under the default arrangement looks pretty good, but the N-terminus needs one of the 243 templates while the C-terminus needs the 250 template. Trying to apply a partial threading to either end, however, will mess up the loops connecting those segments to the rest of the protein. Now, this problem could be solved if there were a way to align the template to part of the protein just like aligning a guide or to move the entire protein in single-piece puzzles as if it were a ligand...