[phenixbb] phenix autobuild and omit map

[rpai at berkeley.edu]

Hi,
I have a loop that was improperly built when I ran autobuild.  the density
according to the Fobs-Fcalc maps is not that great.

Someone told me that autobuild can use omit maps to build / rebuild the
loops so you dont have to do it by hand.

Looking at the manual, I found the command, but am a little confused.

The model used is the entire model correct?
the target.pdb is the chain or region that was not correctly built.
For iterative building...how many cycles should I go for?


phenix.autobuild data=w1.sca model=coords.pdb omit_box_pdb=target.pdb \
   composite_omit_type=iterative_build_omit

thanks
Raj