[phenixbb] paired refinement in phenix gui

Nathaniel Echols nechols at lbl.gov
Mon May 27 15:08:26 PDT 2013

On Mon, May 27, 2013 at 9:54 AM, Georg Mlynek <georg.mlynek at univie.ac.at> wrote:
> It would be nice if you could confirm if my settings are ok, or if there are
> still some settings in the background which I overlooked, because we see
> small changes in R and Rfree.

Changes relative to what?  It is not expected that feeding the output
PDB file back to phenix.refine (or another program) will exactly
reproduce the R-factors from the previous round of refinement, because
the precision of the atomic parameters is limited by PDB format.
(Using mmCIF instead would be more reliable, but we don't think a
change in R-factor of 0.0004 is worth worrying about anyway.)

> I added the model refined at higher resolution (e.g. 1.5A) and the mtz file
> cut at CC (e.g.1.5A) in the “Input data” tab, and set High resolution cutoff
> in “X-ray data and experimental phases” box to (e.g. 1.8A)
> In the refinement setting strategy tab I uncheck everything and set Number
> of cycles = 1.
> In “other options” I uncheck everything too.

This sounds correct, but it's much easier to simply run the validation
GUI, because the underlying code (specifically phenix.model_vs_data)
is designed to calculate identical R-factors to what phenix.refine
shows you.

> Alternatively adding a file to the input data with

I don't recommend this - using parameter files as input is fine for
large repetitive parameter blocks such as custom geometry restraints,
selections from the TLSMD server, or nucleic acid base pairs, but
anything that attempts to override the controls in the main GUI may
not work.

> 2. For whatever reason I would like to do that (molprobity) - can I (and how
> can I do this)  add the command line commands also in the gui?

Could you please clarify?

> 3. In december 2012 there was a discussion about weak data and refinement. I
> would like to know if there are new data available showing that “Whether the
> benefit they describe is considered cosmetic or non-trivial,.....”

Maybe Kay could comment on this...

> 4. Additionally could one short comment on what phenix is doing with strong
> (weak) reflections marked as aliens in XDS.

Assuming that XDS doesn't actually remove these, phenix.refine may or
may not discard them at the outlier filtering stage (which can be
disabled).  I don't know how the different methods for flagging
suspect resolutions compare; Kay and/or Pavel would know more about

> According to the supplementary of P. Andrew Karplus, Kay Diederichs “Linking
> Crystallographic Model and Data Quality”
> I would like to do
> anisotropic refinement, with additional options
> “ordered_solvent.new_solvent=anisotropic
> adp.individual.anisotropic="not element H"
> fix_rotamers=True”.

If your resolution really is 1.5Å, I wouldn't recommend making waters
anisotropic.  There is some difference of opinion whether anisotropic
refinement of protein atoms is acceptable; it's probably good to try
both ways.  (It would be interesting to know whether including the
weak high-resolution data allows you to parameterize the model more


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