Re: [phenixbb] phenix.refine is renaming experimental phase labels and the purpose of _refine_data.mtz?

Hi Francis and Nat, Unfortunately there already is a little discrepancy in the naming of HL coeffs. Resolve does write out HLAM etc as density modified phase information...However the exptl_fobs_freeR_flags_1.mtz from autosol are also labeled HLAM even though they are experimental HL coeffs. I apologize for the lack of consistency there. -Tom T

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On Sat, Sep 3, 2011 at 1:25 PM, Francis E Reyes wrote:

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When specifying exptl_fobs_phases_freeR_flags_1.mtz (HLAM,HLBM.HLCM,HLDM) as an experimental phase file in phenix.refine via the .def file,  these HL coefficients are written to *_refine_data.mtz as HLA,HLB,HLC,HLD.

Now forgive me if I'm incorrect but HLA,HLB,HLC,HLD != HLAM,HLBM,HLCM,HLDM ? (where the former should come from phaser_1.mtz and the latter from resolve_1.mtz reflecting the density modification step).

Phenix doesn't really track column labels internally, or propagate them - it sees Hendrickson-Lattman coefficients, and automatically labels them HL*. The method that handles this isn't even capable of handling "HLAM" without modifying the code - the "A" will always end up at the end. Actually, Phenix doesn't organize data in "columns" either, so it's pretty detached from MTZ format.

I'm not sure what the distinction between HLA and HLAM is - your interpretation sounds correct, but that would mean that AutoSol is writing out the density-modified phases instead of the experimental phases. Which doesn't sound right to me; I guess you could use phaser_1.mtz to be safe.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb