Hi Joe, thanks for the feedback!
If NCS restraint selection in the .def file have newline characters, the REMARK 3 formatting is messed up. It should probably replace all white-space regions with a single space.
Could you please send me an example of such .def and PDB file with bad REMARK 3 records?
When NCS restraints contain a residue with alternate conformations, that residue gets excluded from all equivalences, even if the selections contain ALTID to avoid the redundant atoms.
I'm not sure about this one, I hope Ralf will clarify this. I presume the NCS selection machinery excludes residues in alternative conformations automatically (as it for example does for H atoms)... Ralf, is this true?
If the .def file has a syntax error, phenix.refine dies with an error that the file format is not recognized. Why not print syntax errors?
This one for Ralf too...
The optimize_wxc and optimize_wxu features are useful, but it is difficult to use the result to define an improved fixed scale on subsequent rounds, without having to optimize every time. It is not obvious whether the scale written in the log represents the new wxc_scale, or if it is a multiplier versus the current wxc_scale. The log also truncates to 2 decimal places. In my case, I only get one significant digit from scale=0.05. I propose that the optimizations write something like "Optimal wxc_scale = 0.533".
This is a frequent question that I replied many times. The optimal weight that comes out of "optimize_wxc=true" (or "optimize_wxu=true") may significantly vary (or may not, it depends...) between macro-cycles or between phenix.refine runs. This is why the optimal weight value found at particular macro-cycle is not preserved. I can add an option so it gets preserved in .def file if a user specifically asks for this (adding it to my to-do list). I will change the output to the .log file to make this clear.
The input data is written as "refine_data.mtz", not using the serial number,
If I correctly understood the question... This file is created when you run phenix.refine with 1) multiple files (for example, one file contains Fobs, and the other one contains free-R flags), or 2) non-MTZ file, or 3) your inputs do not contain free-R flags and you asked phenix.refine to create them. If you start with one MTZ file that contains free-R flags, then *_data.mtz is not created. Since this is a one-time operation, the serial number is not appended. Thanks! Pavel.