[phenixbb] questoin about AutoBuild

Thomas C. Terwilliger terwilliger at lanl.gov
Sat Jun 27 16:07:00 PDT 2009

Hi  Qun,

If you say "phenix.autobuild after_autosol" then autobuild will take the
autosol run that gave the highest score, so in your case that seems to
have been #5.

If you want to carry on with a different run, you want to say something like:

 phenix.autobuild data=AutoSol_run_5_/exptl_fobs_freer_flags_3.mtz \
 map_file=AutoSol_run_5_/resolve_3.mtz \

1.  use resolve_xx.mtz as a map file, never as a "data" file. It contains
coefficients for a density-modified map
2. I recommend not including the model from autosol in your autobuild
runs. Autobuild is a lot better at building a model.
3. The data file for autobuild should be
AutoSol_run_5_/exptl_fobs_freer_flags_3.mtz in this case;  note that the
"3" here matches the "3" in resolve_3.mtz and is for solution #3 of run 5.
4. To see what files to use here, see the file
"AutoBuild_run_5_/AutoBuild_summary.dat which lists the solutions for run
5, and all the files that go with each solution.

An aside: I would use the R value and not the Rfree value to make
decisions about which solution to take.  This will help keep the Rfree
"free". It will also give the same result almost all the time.

All the best,
Tom T

>> Deal All,
>> After I tried 9 runs of AutoSol from my MAD data by changing parameters
>> (resolution, heavy atom numbers), I got 9 results, named as:
>> AutoSol_run_1_
>> to AutoSol_run_9_. I found #9 and #7 have the lowest Rfree, so I want to
>> pick the model from these two runs.
>> However, when I use "phenix.autobuild after_autosol", the resulting
>> AutoBuild files tell me that the  program picked the result from #5 of
>> AutoSol, not the lastest #9.
>> Does anyone know how can I specify the exact number of AutoSol to run
>> autobuild?
>> I also tried this command "phenix.autobuild data=resolve_3.mtz
>> model=overall_best.pdb seq_file=zntb-sd.seq"under the directory of
>> AutoSol_run_9_, but failed with the following word:
>> ********************************************************************************
>> Failed to carry out AutoBuild_build_cycle:
>> Initial phenix refinement of
>> AutoBuild_run_2_/TEMP0/NO_LIG_NO_WAT_overall_best_edited.pdb with
>> exptl_fobs_phases_freeR_flags.mtz failed...quitting...
>> See AutoBuild_run_2_/LAST.LOG for more information
>> Please resolve the R-free flags mismatch.
>> ********************************************************************************
>> Does anyone know where is wrong?
>> Qun Wan
>> Department of Pharmacology, Case Western Reserve University
>> 10900 Euclid Avenue, Cleveland, OH 44106
>> email: qunwan1 at gmail.com
>> lab phone: 216-368-3337
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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