[phenixbb] unit cell discrepancies

Dale Tronrud det102 at uoxray.uoregon.edu
Thu Apr 21 12:13:22 PDT 2011

On 04/21/11 11:59, Pavel Afonine wrote:
> Hi,
>>> Actually, this thread raises an interesting issue: do refinement
>>> programs ever refine cell parameters (I think they do not.)
>> Not as far as I'm aware.
> definitely not in phenix.refine.
>>> I wonder
>>> whether it would make any difference, especially in things like bond
>>> lengths? Should be easy enough to include, but I guess the gains might
>>> not be so significant? I would imagine, though, that once one had a
>>> working model, one could make a histogram of observed bond lengths and
>>> their orientations, and scale the cell parameters accordingly to make
>>> the bond-length distribution be centered on the ideal lengths. This
>>> might perhaps be another source of "missing R"?
>> I've never used WHATCHECK, but I'm told it does something like you
>> describe, and alerts the user to possibly incorrect cell dimensions.
>> (I'm hoping to add this to the PHENIX validation eventually, but I
>> don't know the math.)
> Not going into discussion whether this would be beneficial or not, from
> implementation point of view it should be very easy to do: just
> grid-search scan around each unit cell dimension and angle (that can
> deviate) in some small interval and score the result by R-factors.
> I would write a simple Python script that does this (it would be under
> 50 lines using CCTBX tools) and run through the whole PDB. In parallel
> one can do a control experiment by faking Fobs (compute from model in
> some way) and see how small unit cell changes affect the R-factors. A
> nice project for a summer student -:)
   This would not work because the cell constants are highly correlated
with the other parameters in the model.  You have to change the cell,
refine all the other parameters, and then write down the R value.  Many
people have become confused by performing the test you describe.  It shows
a very steep dependency between the R value and the cell constants but
the lowest R value is always at the values for the cell the model was
refined with.  If you perform your grid test and refine at each step
you will see the broad minimum.

Dale Tronrud

> Pavel.
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