[phenixbb] Various problems with phenix.refine

Joe Krahn krahn at niehs.nih.gov
Wed Sep 23 12:04:31 PDT 2009

Here are a few problems I have found using phenix.refine 1.4:

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.

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.

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?

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".

The input data is written as "refine_data.mtz", not using the serial 
number, and there seems to be no flag to disable writing it. That means 
I have to force overwrite to run iterations in the same directory. If 
each run is in its own directory, the serial number is not very useful 
for filenames. So, the output MTZ should have the serial number, and you 
might also consider an option to disable the serial number when separate 
directories are used.

Joe Krahn

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