[phenixbb] phenix.automr questions

Nathaniel Echols nechols at lbl.gov
Sun Aug 29 09:25:29 PDT 2010

On Sun, Aug 29, 2010 at 1:58 AM, Randy J. Read <rjr27 at cam.ac.uk> wrote:
> We were thinking that AutoMR would be the interface for people with
> (relatively) straightforward problems, and that the Phaser-MR GUI would
> allow all of the fine control available from keyword (or indeed Python
> scripting) input. Of course, it might be a good idea to add a few more
> options to AutoMR and we're open to suggestions. If you don't like GUIs,
> there isn't a command-line equivalent to Phaser-MR, but you can always use a
> shell script.

Actually, there *is* a command-line equivalent to Phaser-MR, but it is
undocumented because I didn't think anyone would use it.  And as I
just found out, it is somewhat difficult to figure out how to use.
But if anyone is interested, the attached parameter file shows how to
configure it - it was necessary to do this to get the GUI working but
I also find this syntax easier to use than the old keyword input.  So
if you run this:

phenix.phaser params.eff

it will use the Phenix-style configuration file, but if you just run
"phenix.phaser" with no arguments (or a shell redirect from a file),
it will use the CCP4-style keyword input.

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