[phenixbb] Autobuild combine

Terwilliger, Thomas C terwilliger at lanl.gov
Mon Dec 2 14:56:46 PST 2013

Hi Heather,

I'm sorry for the trouble!  There are two things that you'll need to do and then (hopefully) it should work.

First, you'll need the version of phenix that will be available tomorrow or later (because I had to fix a bug) and second, you'll need to make a very small change to the script below.  In the first autobuild run you'll need to add the keyword "input_map_file=xxxx.mtz" where xxxx.mtz is any map coefficients file (it won't actually be used ).

Let me know if that doesn't do it!

-Tom T

On Dec 2, 2013, at 10:47 AM, Heather L Condurso wrote:

Hi all,

I am still having issues with Autobuild giving errors during the combine step.  I've downloaded the latest build and hope that will solve the problem, but in the mean time I'm having an issue trying to combine the models.

I've been following the script:

#!/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

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


Here are the two log files.  I used the expl_fobs_phases_freeR_flags.mtz as fobs.mtz and changed each overall_best.pdb and overall_best_refine_map_coeffs.mtz as the model and map to combine.



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