[phenixbb] A question about AutoBuild

[Thomas C. Terwilliger]

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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