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

Thomas C. Terwilliger terwilliger at lanl.gov
Fri Dec 28 18:22:08 PST 2007

Hi Dale,

Can you try something else:

phenix.refine    AutoBuild_run_12_/overall_best.pdb \
 AutoBuild_run_12/exptl_fobs_freeR_flags.mtz \
  refinement.main.high_resolution=2.2 refinement.main.low_resolution=20 \

This differs from your run only by substituting


for your 2 refinement data files.  This is the exact file that is used in
refinement by AutoBuild.

I agree that you should be able to use your original data file instead.  A
possible reason why this has failed is that the original data file has a
couple reflections for which there is no data...and which were tossed by
AutoBuild before creating exptl_fobs_freeR_flags.mtz . Two files that
differ only in reflections with no data will still give different
checksums, I think.

All the best,
Tom T

> Hi Dale,
>>> 1) Why you specify reflection MTZ file twice in phenix.refine script?
>>     I put the mtz in twice because if I put it in once phenix.refine
>> complains that I have no free R flags.  It seems to want one file with
>> the amplitudes and another with the flags.  Since I have both in the
>> same file I put that file on the line twice and phenix.refine finds
>> everything it needs.
> phenix.refine looks for free-R flags in your main data file
> (1M50-2.mtz). Optionally you can provide a separate file containing
> free-R flags (I have to write about this in the manual). However, if
> your  1M50-2.mtz contains free-R flags then you don't need to give it
> twice. So clearly something is wrong at this step and we need to find
> out what is wrong before doing anything else. Could you send the result
> of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your
> data file? Or I can debug it myself if you send me the data and model.
>>     If the MD5 hash of the test set depends on the resolution then
>> certainly
>> I could be in trouble.
> No. It must always use the original files before any processing.
>>     Does the resolution limit affect the MD5 hash of the test set?
> No.  If it does then it is a very bad bug. I will play with this myself
> later tonight.
>>> 3) Does this work:
>>> (...)
>>     I'll try these but it will take a bit of time.
> Don't run it until completion. Just make sure it passed through the
> processing step.
> Pavel.
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