[phenixbb] model completion after autobuild

Tom Terwilliger terwilliger at lanl.gov
Fri Mar 6 09:01:02 PST 2009

Hi James,

I'm sorry for the slow reply, I missed your email when you sent it and  
just saw it today.

There are several ways you can try and get autobuild to build just a  
little more.  One is just to put in the last model from the previous  
run in as model=mybestmodel.pdb and specify "rebuild_in_place=false"  
and run it again.

In your case it sounds like you really want to fit a loop. Here is a  
good way to do that:

phenix.autobuild data=mydata.mtz model=model_missing_loop.pdb \
input_map_file=map.mtz seq_file=sequence.dat rebuild_in_place=false \
include_input_model=true number_of_models=0 fit_loops=true \
connect=true build_outside=false insert_helices=False \
helices_strands_start=False n_cycle_rebuild_max=1 \
thorough_loop_fit=true number_of_parallel_models=1

Here the key parameters are fit_loops=true and skipping  
build_outside_model and insert_helices. The connect=true will help if  
you do not have sequence assigned at the ends of your loop.  The   
thorough_loop_fit=true tell it to try hard for the loop.  The  
number_of_models=0 says don't bother to rebuild the model from scratch.

This should run relatively quickly.  It is possible that it will  
"lose" some good parts of your model, so it may be necessary to do  
some splicing if that happens.

All the best,
Tom T

Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
Fax: 505-665-3024                 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

On Mar 3, 2009, at 6:37 AM, James Whittle wrote:

> Dear all,
> AutoBuild has successfully built almost my entire model - I copied
> loops built better in one NCS copy to the other, and now only one 16
> residue loop connecting two helices is missing. It initially built a
> chain through the density for this loop, but could not join it to the
> rest of the structure or place the sequence there, so I deleted it.
> When I re-run autobuild on my modified model, rebuild_in_place=True is
> automatically set and this loop is not completed. The density is
> there, so it should be possible.
> How does one instruct AutoBuild to finish an almost complete model (in
> particular this loop), without much change to the existing model?
> --James
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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