[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 \
rebuild_in_place=Yes
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 \
/usr/users/dale/geometry/chromophores/bcl_tnt.cif
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:
785fd03f6881898dcd91bc5f8c3e5b26
The corresponding MD5 checksum in the PDB file summarized above is:
6f86ee71dbcd2dc1f5282cf18547c79b
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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