"In Phenix the parameter test_flag_value sets the value of the test set that is to be free. Normally Phenix sets up test sets with values of 0 and 1 with 1 as the free set. The CCP4 convention is values of 0 through 19 with 0 as the free set. Either of these is recognized by default in Phenix and you do not need to do anything special. If you have any other convention (for example values of 0 to 19 and test set is 1) then you can specify this with test_flag_value.
Note that phenix.refine and AutoBuild write out PDB files that contain
the test_flag_value. AutoBuild can read this test_flag_value and use it
automatically. However if there is a conflict between this test_flag_value
and the default value based on your data file, you may have to specify which
to use."
So I think the answer is YES.
Best!
Lu Zuokun
Hi Sam,
I��m sure the PHENIX developers will clarify this point, but in any case you could just dump the two MTZ files to text ones:
mtzdump hklin file1.mtz > file1.txtnref -1end
mtzdump hklin file2.mtz > file2.txtnref -1end
and compare whether the same reflections are flagged in both.
HTH,
Luca
On 12 May 2016, at 04:59, Sam Tang <samtys0910@GMAIL.COM> wrote:
Dear all_______________________________________________
May I enquire a simple question about AutoBuild - I input an experimental data (ccp4 mtz from Aimless) and a model from Phaser-MR to AutoBuild hoping that some mis-fit flexible regions could be re-build. May I know if the output mtz overall_best_refine_data.mtz contains the same FreeR flags as in the input, or would AutoBuild generate a new set of FreeR? Or in other words, are the R values directly comparable if I refine against the input experimental data mtz or the overall_best_refine_data.mtz?
Thanks!
Cheers
Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK
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