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@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:
LABIN F = F SIGF = 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

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