[phenixbb] unit cell discrepancies

Pavel Afonine pafonine at lbl.gov
Thu Apr 21 11:59:31 PDT 2011


>> 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 -:)


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