Hi Marcelo, Rebuilding in place means "take the existing model and try to adjust it by local rebuilding to fit the density better" (...and add water molecules to unexplained density). I think that the name leaves something to be desired, but the procedure works well when you have pretty much the whole thing and you just want to make a better model. In your case, it would be best to put in the model, but to let AutoBuild build the remainder of the structure from the map. Best regards, Tom T .> We have solved (in part) a structure by Molecular Replacement. The

protein is a homodimer with 360 amino acids per chain (one dimmer per asu). The model was pretty good for the last 220 amino acids or so but appears to be wrong for the first 140 so I deleted them and refined using phenix to an R free of ~ 0.38. As I was about to start model building in O I thought I would give the phenix autobuild a try.

The resolution is 2.5 Å and the map shows buildable features for the missing domain. I ran the autobuild wizard with RESOLVE building “in- place” to extend the current model. However the program seemed unable to add fragments of secondary structure (even as alanines) to the model. The question is: is the building “in-place” restricted to “growing” the current model from the ends?

Marcelo

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb