[phenixbb] Using the Same Test Set in AutoBuild and Phenix.Refine

Dale Tronrud det102 at uoxray.uoregon.edu
Fri Dec 28 14:14:25 PST 2007

Hi all,

    I have another problem, I'm afraid.  I have built a model using
phenix.autobuild and now want to run some refinement.  While in the
long run I'll do some manually rebuilding using Coot I just wanted
to run a test of phenix.refine to ensure I have the script right and
have a baseline to compare against later.

    My autobuild script is:

phenix.autobuild model=AutoMR_run_4_/MR.1-protein.pdb data=1M50-2.mtz \
   input_refinement_labels="FP SIGFP None None None None None None FreeR_flag" \
                  map_file=AutoMR_run_4_/MR.MAP_COEFFS.1.mtz \
                  seq_file=../fmo-ct.pir \
                  resolution=2.2 dmax=20 refinement_resolution=2.2 \
                  cif_def_file_list=/usr/users/dale/geometry/chromophores/bcl_tnt.cif \
                  input_lig_file_list=AutoMR_run_4_/MR.1-Bchl-a.pdb \

    My refine script is

phenix.refine    AutoBuild_run_12_/overall_best.pdb \
                  refinement.input.xray_data.file_name=1M50-2.mtz 1M50-2.mtz \
                  refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \

    As you can guess, my test set flags are in the same mtz file as the
amplitudes.  I'm feeding exactly the same file into both runs.  Despite
this I get in my output


The MD5 checksum for the R-free flags array summarized above is:

The corresponding MD5 checksum in the PDB file summarized above is:

These checksums should be identical but are in fact different. This is
because the R-free flags used at previous stages of refinement are
different from the R-free flags summarized above. As a consequence,
the values for R-free will be biased and misleading. It is best to
avoid this situation by consistently using the same R-free flags
throughout the refinement of a model. If the previously used R-free
flags are still available run this command again with the name of the
file containing the original flags as an additional input.

If the original R-free flags are unrecoverable, remove the

   REMARK r_free_flags.md5.hexdigest 6f86ee71dbcd2dc1f5282cf18547c79b

record from the input PDB file to proceed with the refinement. In
this case the values for R-free will become meaningful only after
many cycles of refinement.


Sorry: Please resolve the R-free flags mismatch.

    While I'm glad that Phenix is checking to ensure that I haven't
goofed and tried to switch test sets, I believe I'm being unjustly
accused.  Why does phenix.refine think I'm a bad boy?

Dale Tronrud

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