[phenixbb] phenix.phaser params.eff labin problem

Nathaniel Echols nechols at lbl.gov
Tue Jul 19 08:47:21 PDT 2011

On Tue, Jul 19, 2011 at 3:13 AM, G P <gysubscribe at gmail.com> wrote:
> I am now writing a script for phenix.phaser.
> In the input file params.eff there is a keyword labin which corresponds to
> the labels inside input mtz files. The important columns in my ccp4 mtz file
> are FP, SIGFP.
> I edit the line of labin as:
> when running the script, it returns me: Syntax error: expected "=", found
> "F" (file "params.eff", line 9)
> So, I changed it like:
> labin=FP SIGFP
> when running, it gave me the message: Sorry: Couldn't find array FP SIGP in
> file
> I also tried: labin="FP" or labin = "FP SIGFP" or labin="labin F=FP" and so
> on. With nothing it can find the right columns.
> My mtz file should be not problem, I checked with mtzdmp, the columns FP and
> SIGFP were there and with phenix GUI this file works well.
> Would someone know exactly how to edit this line in params.eff?


The syntax used for these parameter files is much different from the
CCP4 keyword input - this was necessary for incorporating Phaser into
the Phenix GUI.  Among other things, we specify data labels in groups,
and internally "FP,SIGFP" is a single data structure containing both
the amplitudes and sigmas.  FYI, unlike the CCP4 version, with
phenix.phaser you can use any type of data as input, so an anomalous
Scalepack file will work too.  (Of course you still need to know what
labels to use - someday I intend to make the setup more automatic on
the command line.)


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