[phenixbb] phenix.phaser params.eff labin problem

G P gysubscribe at gmail.com
Wed Jul 20 03:18:24 PDT 2011

Thanks a lot Nat!

I tried exactly what you suggested. Still it returned me could not find the
labels.  I also tried labin = "FP,SIGFP" and labin="FP, SIGFP" and
other possiblities with or withour space in between. They all returned me
could not find the label FP, SIGFP.

Should I give the keyword in capital letters. Or may be I should try other
format input file? I do not care about anomalous signal in this data,
because I will just use MR_AUTO model in phenix.phaser.

Any other ideas would be greatly appreciated. Thanks again for your time.

Best regards,

On Tue, Jul 19, 2011 at 5:47 PM, Nathaniel Echols <nechols at lbl.gov> wrote:

> 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:
> > labin F=FP SIGF=SIGFP
> > 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?
> labin="FP,SIGFP"
> 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.)
> -Nat
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