[phenixbb] A question about AutoBuild

Thomas C. Terwilliger terwilliger at lanl.gov
Mon Jul 30 18:01:20 PDT 2007

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
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