[phenixbb] unit cell discrepancies

Edward A. Berry BerryE at upstate.edu
Thu Apr 21 13:08:15 PDT 2011

Nathaniel Echols wrote:
> 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.)

>> 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.)

Using whatcheck for this leads to the kind of wild goose chase that
Dale Tronrud was describing, but I was given to understand the reason
is that whatcheck uses a different version of the Engh&Huber values than
the refinement program i was using does.  I think minimizing the RMSD bond
lengths as a function of the three cell edges given fractional coordinates,
alternating with regular positional refinement, should converge very quickly.

As Dale says the R-factor is not very sensitive, I chased the cell edges
through several percent change without affecting R much.

More information about the phenixbb mailing list