[phenixbb] question about autobuild

Tom Terwilliger terwilliger at lanl.gov
Thu Sep 3 09:36:42 PDT 2009


You can supply the model from the first run to phenix.autobuild and it  
will start from there.  You want to say "rebuild_in_place=False" so  
that autobuild knows you want to add more residues, not to just adjust  
the ones you have supplied.  You will also want to supply the same  
freeR set that was used in the first run. If you provided freeR flags  
in your input datafile, use that again. If phenix.autobuild generated  
them, then you want to use "data= AutoBuild_run_1_/ 

phenix.autobuild data=data_with_freeR_set.mtz \
   model=model_from_run_1.pdb \
   seq_file=seq.dat \

All the best,
Tom T

On Sep 3, 2009, at 10:30 AM, crystallogrphy wrote:

> Hi,
> I have used phenix.automr followed by phenix.autobuild to build a  
> 264 residue model against my 2.1A resolution data set. The first run  
> of autobuild gives me about 180 residues built. I have adjusted the  
> model according to the denity. The N-terminal of the model has OK  
> density to add more residues to the model. Can phenix.autobuild has  
> some command to just put more residues to the N-terminal of my  
> current model according to the density, so that the cost of CPU time  
> will be much less than rerun the job completely?
> Thanks!
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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

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