[phenixbb] Reflection file woes phenix/ccp4/PDB

Robert Immormino immormino at gmail.com
Thu Dec 15 09:05:32 PST 2011

Hi Mischa,
It may be helpful to share the header and first several lines of the
.mtz.  There might be something weird about the column labels that's
causing the problem.

On Thu, Dec 15, 2011 at 11:40 AM, Machius, Mischa Christian
<mischa_machius at med.unc.edu> wrote:
> Y'all,
> While depositing a structure, the PDB 'complained' about my structure-factor file, saying they don't contain R-free flags or are otherwise incomplete. The comment was prompted by their Refmac R-factor test failing.
> The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928.
> 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"
> The file contains anomalous data. I have no problems with files that do not contain anomalous data.
> Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility.
> When I use  iotbx.reflection_file_reader, I cannot detect any anomalies.
> I am at a loss as to how to resolve this issue. I would like to deposit the data as prepared by Phenix so that the PDB tools can use them.
> Anybody ran into this issue before? Any ideas for how to resolve it?
> Many thanks in advance!
> MM
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