[phenixbb] unit cell discrepancies

Nathaniel Echols nechols at lbl.gov
Thu Apr 21 11:35:39 PDT 2011

On Thu, Apr 21, 2011 at 11:21 AM, Jacob Keller
<j-keller2 at fsm.northwestern.edu> wrote:
> 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.

> 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.)  Packing analysis can also give similar
indications that something is wrong:


But I think the error needs to be much larger than you're likely to
get from processing the data for the refinement to suffer
significantly.  It definitely doesn't explain the discrepancy in
R-factors, since even an excellent protein crystal diffracting to
atomic resolution - where there is no doubt as to the unit cell
parameters - will still have this problem.


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