Re: [phenixbb] unit cell discrepancies

Nathaniel Echols wrote:

On Thu, Apr 21, 2011 at 11:21 AM, Jacob Keller wrote:

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Actually, this thread raises an interesting issue: do refinement programs ever refine cell parameters (I think they do not.)

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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.