[phenixbb] Autobuild parent process aborted--running combine_models in Autobuild

Thomas C. Terwilliger terwilliger at lanl.gov
Tue Mar 22 18:35:05 PDT 2011

Hi Mark,

The answer depends on whether this is a "rebuild_in_place=True" run or
not.  (I think you are using rebuild_in_place=true, but I'll give both

Assuming "rebuild_in_place=True":

You can combine models with autobuild, providing all models have exactly
the same set of atoms (aside from any solvent) by editing this script
(basically you run a dummy autobuild run to create a directory and
database entries, then you copy your files there, then you run autobuild
and tell it to carry on and do the combine step):

#!/bin/csh -f

if (-d PDS || -d AutoBuild_run_1_) then
  echo "Please run in a directory without PDS or AutoBuild_run_1_"
  exit 1

echo "Setting up combine models with a dummy run. NOTE:
multiple_models_group_number must be correct"

phenix.autobuild fobs.mtz multiple_models=true seq_file=seq.dat
combine_only=true multiple_models_group_number=2
multiple_models_number=1>& dummy_autobuild.log

echo "Copying files to AutoBuild_run_1_/MULTIPLE_MODELS"
mkdir AutoBuild_run_1_/MULTIPLE_MODELS
cp coords1.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_1
cp coords2.pdb AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.pdb_1_2
cp map_coeffs_1.mtz  AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_1
cp map_coeffs_2.mtz  AutoBuild_run_1_/MULTIPLE_MODELS/initial_model.mtz_1_2

ls AutoBuild_run_1_/MULTIPLE_MODELS/

echo "Running autobuild to combine files in AutoBuild_run_1_/MULTIPLE_MODELS"

phenix.autobuild combine_only=true seq_file=seq.dat carry_on=true run=1 >


Assuming "rebuild_in_place=False":  In this case you can provide autobuild
with a list of files with consider_main_chain_list="file1.pdb file2.pdb" ,
or simply dump all the models into a singe pdb file and use
model=all_models.pdb, and run autobuild one more time.

Let me know if that doesn't do it!

On Mar 22, 2011, at 3:00 PM, Mark A Saper wrote:

I ran AutoBuild from command line and it submitted 5 jobs with qsub. 
Apparently I aborted the parent process.  So I have the 5 jobs running,
apparently producing 5 different models (I specified nproc = 5 as
suggested in the documentation).  Can I rerun AutoBuild and have it
combine the 5 models already calculated?

Mark A. Saper, Ph.D.
saper at umich.edu     phone (734) 764-3353     fax (734) 764-3323

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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:
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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