[phenixbb] sca file & anomalous difference map: understanding the story from the scratch,

Nathaniel Echols nechols at lbl.gov
Mon Jun 13 10:02:46 PDT 2011

On Mon, Jun 13, 2011 at 8:59 AM, Haytham Wahba <haytham_wahba at yahoo.com>wrote:

> you payed my attention to something i did
> in first round of refinment after molecular replacment
> i used
> 1- output.sca
> 2- MR.1.pdb
> 3- MR.1.mtz
> as input files
> then i proceded with the output of this round of refinment to other
> because you sayed ((do not use MR.mtz for refinement!*))
> 1- in this case should i start agian from the begining or it does not
> matter because .sca was included.
> 2- how can i know form the output files of this first run, if both .sca and
> MR.1.mtz were used or only one was used in refinment

I just tried this, and if you added the Scalepack file first (which, FYI,
would get done for you automatically if you clicked the "Run phenix.refine"
button in the AutoMR or Phaser GUIs), then MR.1.mtz will be used as
experimental phase restraints, but nothing else.  This isn't appropriate
(you should only use genuine experimental phases for this, not model-based
phases), but it doesn't negate the results of the refinement.  However, you
really need to look at the log file from refinement to be certain - it will
state which parameters each reflection file were used for.  Could you please
send the log to nechols at lbl.gov (not the entire list)?

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