[phenixbb] reflection file converter

Nathaniel Echols nechols at lbl.gov
Wed Nov 17 11:47:53 PST 2010

On Wed, Nov 17, 2010 at 9:41 AM, r n <ramme29 at yahoo.com> wrote:
> I did tried reflection file converter in phenix. I do have the anomalous
data, like to keep all anomalous difference and also
> merged  F and FreeR for refinement.
> Phenix GUI give me an warning message that
> "File are not suitable for amplitudes change them as F or leave them as

This means that you've changed the output type to amplitudes, but the labels
still look like intensities (i.e. I, SIGI, etc.).  If you are converting to
merged amplitudes, then the output labels should be just F and SIGF (in that
order).  For what you're specifically trying to do, you will need to run it
twice, once to generate F,SIGF (and FreeR_flags), and again to combine the
output of the first run with the anomalous intensities.

> Also have hard time to convert them in command line, Is there any auto
script that can work similar to scaelpack2mtz ,  which keeps all I+, I- and
F , SigF, Rfree for refinement.

It's a little difficult to do this automatically right now.  One reason is
that Phenix doesn't deal very intuitively with MTZ columns (the units of
data we work with - "Miller arrays" - are typically multiple columns grouped
together).  The other is that the reflection file editor is really meant to
combine different data types, and doesn't do the sort of multi-step
conversion that scalepack2mtz does.  It would be trivial to add this feature
as a simple black-box GUI widget (and command-line program) - I'll throw
something together the next time I have a few hours free.  The reflection
file editor was really intended for operations like combining multiple
datasets and manipulating R-free; merging and converting intensities was
more of an afterthought.

There is one other key difference: scalepack2mtz also includes the
French&Wilson data massaging in the program TRUNCATE, which guesses
appropriate values for negative intensities.  (I may be getting this
slightly wrong; I never understood what this step does.)  We don't have
anything to do that in Phenix.  Whether you actually need this is a matter
of personal opinion, however.

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