[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
Can you try something else:
phenix.refine AutoBuild_run_12_/overall_best.pdb \
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,
> 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
>> 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.
> phenixbb mailing list
> phenixbb at phenix-online.org
More information about the phenixbb