[phenixbb] Request: read definitions from stdin

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Fri Nov 13 09:12:24 PST 2009

The --quiet option exists (phenix.refine --help). Reading from
stdin is too tricky as a general feature ("my job hangs") and since
phenix.refine cannot work without reading from files (pdb, mtz) and
writes many files already, that one extra file doesn't really make
a difference.
However, you can script phenix.refine from Python, see
phenix/phenix/refinement/command_line.py, the run() function, and
pass in a list of "external_params", which you could read from stdin.
To find out how to pre-process the external_params, see:

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