[phenixbb] Reflection file woes phenix/ccp4/PDB

Ed Pozharski epozh001 at umaryland.edu
Thu Dec 15 09:05:30 PST 2011

On Thu, 2011-12-15 at 16:40 +0000, Machius, Mischa Christian wrote:
> Indeed, using this file in CCP4 fails with the message: 
> "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J  CCP4MTZfile: Mtz
> column type mismatch: SIGI-obs(+) M-Q"

According to this


the I-obs(+) column should be type K, and SIGI-obs(+) of type M.  It's
possible that phenix does not follow that convention.

As for R-free flags, did you generate them in phenix?  If so, the refmac
run with default parameters that pdb does during validation would run
against about 5% of reflections (in phenix test_value=1, in refmac it's

I guess general way to avoid such calamity is to generate test set with
freeflag initially.  At this point, you can definitely use something
like sftools to reset the flags so that your model passes pdb validation
with flying colors.



"I'd jump in myself, if I weren't so good at whistling."
                               Julian, King of Lemurs

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