Hi Carsten,
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.
That parameter wasn't actually used. I just removed it completely. Thanks for alerting us to this.
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?
OK, done! You will see the change in the next release (hopefully very soon). Ralf