[phenixbb] Various problems with phenix.refine

Pavel Afonine PAfonine at lbl.gov
Wed Sep 23 12:23:24 PDT 2009

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.


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