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

Pavel Afonine pafonine at lbl.gov
Fri Dec 28 16:40:41 PST 2007

Hi Dale,

1) Why you specify reflection MTZ file twice in phenix.refine script?

2) Try exactly the same Autobuild and phenix.refine runs but without any 
resolution limits. Is it still crashing in this case? The guess is that 
it could be a bug somewhere that causes MD5 calculation on processed 
data file (with resolution cutoffs applied) and then this "wrong" MD5 
record goes into overall_best.pdb and causes inconsistency when compared 
with native 1M50-2.mtz when you start phenix.refine. Again, this is just 
a guess...

3) Does this work:

phenix.refine MR.1-protein.pdb 1M50-2.mtz output.prefix=junk
phenix.refine junk_001.pdb 1M50-2.mtz

phenix.refine MR.1-protein.pdb 1M50-2.mtz output.prefix=junk 
xray_data.high_res=2.2 xray_data.low_res=20
phenix.refine junk_001.pdb 1M50-2.mtz

phenix.refine MR.1-protein.pdb 1M50-2.mtz output.prefix=junk
phenix.refine junk_001.pdb 1M50-2.mtz xray_data.high_res=2.2 


PS> I will be away Dec, 30 - Jan, 1. I will have no email access during 
this time.
Tom is unreachable Jan 1 - 21.

Dale Tronrud wrote:
> 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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