[phenixbb] phaser.labin not respected

Murpholino Peligro murpholinox at gmail.com
Thu Jan 19 10:25:46 PST 2017

OK. Thanks.
...I thought it was selecting the other set of labels by default. It is
good to know it works only with the Fmean :P

2017-01-19 3:31 GMT-06:00 Randy Read <rjr27 at cam.ac.uk>:

> Hi,
> I can see that this could be slightly confusing!  It's explained if you
> give the command "phenix.phaser --help", which returns the following:
> Usage:
> phenix.phaser is a multi-function command: it can launch either the binary
> version, which accepts CCP4-style keyword input, or the Python version,
> which
> uses the standard Phenix configuration file syntax.  If called with no
> arguments or the recognized command-line flags, the binary will be
> launched;
> if a valid Phenix configuration file is provided on the command line, it
> will run the Python version.
> CCP4 style:
>   phenix.phaser
>   phenix.phaser [--version]
>   phenix.phaser [--changelog]
> Phenix style:
>   phenix.phaser [params.eff] [<param_name>=<param_value> ...]
>   phenix.phaser —show_defaults
> So, "phenix.phaser" is a launcher that behaves differently depending on
> how you run it!  The way you've run it, it is being run as a Python script
> that reads the input through Python and passes it, in the form of Python
> objects, to the Phaser routines.  So, in fact, by the time the data gets to
> Phaser through the command-line flags, it's not being passed in the form of
> an MTZ file.  That's why the log file doesn't record the name of the MTZ
> file either.
> I don't usually run Phaser this way myself, so I was actually surprised to
> see that this works!  For molecular replacement, Phaser requires the mean F
> (or preferably the mean intensity), not the Friedel pairs.  The script is
> using the phenix reflection file reader, which can do things like take F+
> and F- and merge them to give Fmean, which is what is actually passed to
> Phaser.
> I hope that helps!
> Best wishes,
> Randy Read
> On 19 Jan 2017, at 03:40, Murpholino Peligro <murpholinox at gmail.com>
> wrote:
> When I do in the terminal:
> phenix.phaser phaser.hklin="out.mtz" phaser.labin="F(+),SIGF(+),F(-),SIGF(-),merged"
> phaser.model="prot.pdb" phaser.mol_weight=14400 phaser.model_rmsd=0.3
> my log file says it is using F and SIGF:
> Why it does not respect the labels provided? or..Am I doing something
> wrong.
> PS MR is successful
> Thanks
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> ------
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical Research      Tel: + 44 1223 336500
> Wellcome Trust/MRC Building                   Fax: + 44 1223 336827
> Hills Road                                    E-mail: rjr27 at cam.ac.uk
> Cambridge CB2 0XY, U.K.                       www-structmed.cimr.cam.ac.uk
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