[phenixbb] Various problems with phenix.refine
PAfonine at lbl.gov
Wed Sep 23 12:23:24 PDT 2009
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
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.
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