[phenixbb] Question/enhancement request for automated datafile conversion

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Wed Feb 6 12:21:04 PST 2008


I noticed that there is a possible inconsistency in the handling of xray datafiles in phenix. For instance, we usually invoke phenix like this:

phenix.refine my.sca my.pdb my.def

The .sca file (or dtrek .ref) file gets automatically converted to a mtz file with I-obs and SIGI-obs and refinement proceeds as expected. I just noticed that in the following ...002.def file and in the 001.eff file the parameter xray_data.observation_type is set to amplitude instead of intensities. What is going on there, is phenix smart enough to know when it deals with amplitudes vs. intensities? Did not seem to have much effect on the refinement though when I switched this around, which is surprising.

As an enhancement request: Would it be possible that the autoconversion writes out a mtz file which contains BOTH amplitudes and intensities instead of intensities and R-flags alone? Sometimes it happens that I need to go back to running phaser when the initial rigid body refinement does not grip. Since phaser just runs on amplitudes I need to add a couple of extra steps to get a file, which is useful for both programs. I think the underlying philosophy should be that once data has been imported into the phenix suite, from whichever entry point, it should be usable w/o conversion in all applications. 



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