If you're referring to the trim function… I would say "close, but not quite."
Here's why: When a protein in the standalone client is trimmed, the ends are fixed to prevent the hidden parts from being affected. This is still not quite the same as literally cutting the protein into two or more pieces that can be moved independent of each other.
Yes, but if you do so distances and positions between start and end segemtns of edited part can be changed. Then overall structure will collapse when merged. Or it need use some ugly strech&rebuild to fit pieces back together - score will drop rapidly.
Trim would be enough. Just trim another part (longer) and work on it. Need focus? Trim only few segments and wiggle them to death.
Good point. However… I vaguely remember that Rosetta has several protocols, such as something called CCD ("cyclic coordinate descent"), that could be used to close the gaps created by the usage of cut-points.
For the purpose of foldit implementation, I would imagine that a method similar to what's being used by the alignment tool for filling in gaps could be used– namely, it would try to close the gap via a loop rebuild if possible, and tell you that the gap is too wide to be closable if it fails.
Closing old case since the alignment tool in the developer preview now uses cutpoints.