On Thursday, October 21, 2010 11:38:55 am Jacob Keller wrote:
>
> "if the data really looks like P21--" what are the criteria for that?
This is a straightforward statistical question.
In testing for a possible 2-fold, you want to know:
Do two random reflections related by the putative 2-fold agree with
each other better than two random reflections not related by the
putative 2-fold?
To make this test less sensitive to scaling, one can formulate it
as a correlation coefficient. Have a look at the paper describing
`pointless`.
P Evans (2006), Acta Cryst. D62: 72-82
Testing the for systematic absences indicating a screw axis can also
be phrased as a statistical test, although generally there are a relatively
small number of putative absences to inspect so the test is not all that
strong.
Ethan
> I believe p1 can have good-as-perfect 90deg angles, no?
Correct. The cell angles don't really enter into it.
> And also
> equal cell dimensions? So I don't think you will be able to tell from the
> positions of the spots on the detector, necessarily. Also, would it not be
> more rigorous to say "I can gain a lot by assuming these molecules are in
> p21?" Look, nobody thinks that every molecule in the crystal is identical,
> so that is truly a convenient assumption. The symmetry, I think, is a
> similar assumption at a different level.
>
> By the way, I have always wondered whether anybody has looked into the
> degree of intermolecular differences possible given all of the parameters in
> our crystallographic models. In other words, would a microscopic observer
> look at the molecules in the crystal and see what looks like a crowd from a
> NYC street, or something more like an army formation? How much variety is
> there at the molecular lever, I wonder?
>
> > True: but how do you judge that those differences are within or
> > outside of experimental noise?
>
> Agreed!
>
> > What if by refining in P1 the parametrisation makes those side-chains
> > different in the first place? A poorly defined Lys side-chain suddenly
> > becomes two significantly different poorly defined side-chain?
>
> I don't know--depends on last question I think.
>
> Jacob
>
> *******************************************
> Jacob Pearson Keller
> Northwestern University
> Medical Scientist Training Program
> Dallos Laboratory
> F. Searle 1-240
> 2240 Campus Drive
> Evanston IL 60208
> lab: 847.491.2438
> cel: 773.608.9185
> email: j-kell...@northwestern.edu
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>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742
