beta_helix Staff Lv 1
We realize how difficult this particular CASP 9 target is, but this was one of the cases that every group at CASP 9 had trouble with:
http://predictioncenter.org/casp9/results.cgi?view=tables&target=T0552-D1&model=1&groups_id=
The top prediction was only able to get a GDT ~61 (meaning only ~60% of their prediction matched the native). As mentioned in the comments for 542: http://fold.it/portal/node/992351#comment-16742
the native was solved using NMR and the ensemble of models has a lot of variation.
For this reason we have just provided you with the native guide for model 1 of the NMR ensemble and we have not minimized the structure at all. Do not feel like you have to match the guide perfectly (since you can see in the .gif, from the link, that there is a lot of variation) but it should give you a general idea of where the native is, especially when you are trying to find the best alignment.
In terms of the best alignment, the one we have given you is what our bioinformatic tools tell us is the "ideal alignment", but we are confident that you can find a slightly different alignment that allows you to match the native guide more closely, resulting in less cutpoint massaging (although obviously with this target a lot of massaging is still very necessary).