[phenixbb] phenix.phaser params.eff labin problem

G P gysubscribe at gmail.com
Wed Jul 20 03:46:28 PDT 2011

Hi Nat,

Now I can make it. I just type labin="FP,SIGFP,DANO,SIGDANO". Then there is
no error to find the labels. I think because I should give all columns

But there is another problem. When I run the script, it shows me:

File "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py",
line 694, in __init__
    assert os.path.isfile(params.phaser.solution)
File "/usr/local/phenix-1.7.1-743/phaser/phaser/phenix_interface/driver.py",
line 694, in __init__
    assert os.path.isfile(params.phaser.solution)

Just stop at this step. What would be the reason and how to fix it? Any idea
would be greatly appreciated.

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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20110720/20eb3be8/attachment.htm>

More information about the phenixbb mailing list