[phenixbb] phenix autobuild and omit map

Michael Sawaya sawaya at mbi.ucla.edu
Mon Apr 6 19:12:18 PDT 2009

Hi Raj,

Try this command:
phenix.autobuild data=data.mtz model=coords.pdb 

Coords.pdb should correspond to the best model you have so far.


rpai at berkeley.edu wrote:
> 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
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