[phenixbb] Various problems with phenix.refine

Joe Krahn krahn at niehs.nih.gov
Fri Sep 25 09:21:40 PDT 2009

Ralf W. Grosse-Kunstleve wrote:
>> 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?
> It is a side-effect of automatically recognizing all file formats. We
> give up only after trying each and every possible reader. If nothing
> works, we don't have a mechanism to score what the file is most likely
> and then produce the format-specific error. Solving that problem is
> harder than it may seem at first sight.
> You can get the syntax error via
> iotbx.phil your.def
> Ralf

OK, I understand the difficulty with the "try all input filters" method. 
Here is one way that may work without too much difficulty. Allow the 
file-input procedures to return a diagnostic text if it thinks the file 
is a match, but has errors. If they all fail, but only one file-reader 
returns a message, print it.

A simple short-term solution might be to print a suggestion based on 
just the filename extension, such as your suggestion above. For example, 
*.mtz files could suggest running "mtzdmp file.mtz".


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