[phenixbb] phenix.autobuild

Tom Terwilliger terwilliger at lanl.gov
Wed Oct 22 15:32:56 PDT 2008

Hi Matt,

I think that your run is the "one-good-model' protocol, in which case  
there are by default 5 runs of rebuilding the model and they are then  
combined into a single model. Autobuild one-good-model does take a  
long time, but this seems a bit longer than usual. This could be due  
to the simulated annealing that you are doing...

I had a look at our standard structures in the PHENIX structure  
library and pulled out some examples to give you some examples of how  
long the procedure can take. These do not include simulated annealing:

rh-dehalogenase rebuilds 290 residues at 2.8 A  and takes 3 hours  
(starting R/Rfree =  0.17/0.23 ; final =  0.15/0.21)

a2u-globulin at 2.4 A, four chains each with 157 residues, takes 13  
hours to run rebuild-in-place (R/Rfree= 0.31/0.35 starting; 0.20/0.24  

apoferritin at 2.0 A; 173 residues; takes 26 hours  (R/Rfree=   
0.23/0.26 starting; 0.22/0.25 final)

So overall I'd say your case is on the long side but is probably doing  
what it is supposed to do.  To check it out, have a look at your log  


which is the first of 5 rebuild-in-place runs on your model.   
(AutoBuild runs itself in the TEMP0 subdirectory, yielding all the  
AutoBuild_run_1_ runs there, then the resulting models get combined  
into a final model which goes in top AutoBuild_run_1_/overall_best.pdb).

See if the first run has improved the model and the R/Rfree...Your  
starting R/Rfree before rebuilding will look like this:

Refining model:  unrefined.pdb_1
Model: refine.pdb_1  R/Rfree=0.31/0.35

..and the end of the file will look like this:

  1         2      0.22        0.26      573       0
  2         3      0.21        0.24      577       0
  3         4      0.21        0.24      598       0

so in this case (a2u-globulin) this single rebuild-in-place works  
well...then combining the 5 models from 5 such runs gives the final R/ 
Rfree of 0.20/0.24 I mention above.

I hope that helps!
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 Oct 22, 2008, at 2:55 PM, Matthew Chu wrote:

> Dear all,
> I tried to rebuild my structure from a refined model (by refmac) by  
> phenix.autobuild. I am not sure if it runs properly since this is my  
> first time to run this module....it took like almost a day to just  
> finish the run_1 (there should be five runs by default?), which  
> means it will take me another 4 days to finish the whole thing. My  
> protein has around 350 residues and in the refined model, I have  
> omitted some loops (about 80 residues)  because I cannot see the  
> electron density of those regions. I have put the seq.dat file with  
> the full sequence (~350 residues) and the commands "place_water=Yes"  
> and "s_annealing=True". The resolution is 2.4 A. Should it be taken  
> so long to run?
> Thanks in advance!
> Kind regards,
> Matt
> -- 
> ----------------------------------------------------------------------------
> Matthew LH Chu
> PhD Student
> School of Pharmacy and Pharmaceutical Sciences
> University of Manchester
> ----------------------------------------------------------------------------
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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