[phenixbb] autobuild mistake

Heather L Condurso condurso at bc.edu
Wed Oct 23 07:11:18 PDT 2013

So I was running autobuild on the command line with:

phenix.autobuild data=data.mtz model=model.pdb rebuild_in_place=False

I have a model from another data set that is missing some loops and new
data sets which I would like to use autobuild to see if the model can be

I am using 1.8.4-1496 on a mac with osx 10.6.8.  I was an idiot and when
looking in the directory to check out one of the RUN_FILE_#.log files, I
accidentally clicked on the RUN_FILE executable which started another
AutoBuild subprocess.  Since then all the other subprocesses had finished,
but overall run stalled at:

Splitting work into 4 jobs and running with 1 processors using sh
background=False in ./AutoBuild_run_6_/TEMP0
Final job will be run with sh  with background=True
Starting job 1...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_8.log
Starting job 2...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_9.log
Starting job 3...Log will be: ./AutoBuild_run_6_/TEMP0/RUN_FILE_10.log
Starting job 4...Log will be:  ./AutoBuild_run_6_/TEMP0/RUN_FILE_11.log

And the combine and extend didn't happen.  I saw a post about combining
models from autobuild but it was for rebuild_in_place=True and the post
mentioned that the models needed to have identical sequences for it to
work.  Is there a way to save my mistake without starting over?

The run I had restarted had yielded Rs=999.9 so If there is a way to maybe
combine just 3 of the 4 that may be helpful as well.

Heather Condurso
condurso at bc.edu
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