[phenixbb] A question about AutoBuild

Marcelo Carlos Sousa Marcelo.Sousa at Colorado.EDU
Mon Jul 30 14:37:09 PDT 2007

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?


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