[phenixbb] phenix autobuild and omit map

Tom Terwilliger terwilliger at lanl.gov
Tue Apr 7 07:29:07 PDT 2009

Hi Raj,

Yes, autobuild can make an omit map excluding the region defined by  
your loop, and it can use that map in rebuilding the loop.   The  
command you list below will do that.
> 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?

That is correct.
> the target.pdb is the chain or region that was not correctly built.

Yes, that's right.

> For iterative building...how many cycles should I go for?

A few cycles should do everything that will happen...say 2-4 cycles.
> phenix.autobuild data=w1.sca model=coords.pdb  
> omit_box_pdb=target.pdb \
>   composite_omit_type=iterative_build_omit

Note that this command was designed to make the omit map, omitting the  
target.pdb-defined region...however it will indeed rebuild your model  
in this region. It will set occupancies to 0.0 for atoms in the omit  
region and not include them in refinement as well.

If you want you can take the resolve_composite_map.mtz from this omit  
procedure and use it as an input_map_file in a separate run of  
autobuild, with 1 cycle of rebuilding, to refine the model.

Or you can just run phenix.refine on the model and data, after setting  
the occupancies back to 1.0.

All the best,
Tom T

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