Dear Experts,
At the risk of exposing excess ignorance, truncate makes me
very nervous because I don't quite get exactly what it is
doing with my data and what its assumptions are.
>From the documentation:
========================================================
... the "truncate" procedure (keyword TRUNCATE YES, the
default) calculates a best estimate of F from I, sd(I), and
the distribution of intensities in resolution shells (see
below). This has the effect of forcing all negative
observations to be positive, and inflating the weakest
reflections (less than about 3 sd), because an observation
significantly smaller than the average intensity is likely
to be underestimated.
=========================================================
But is it really true, with data from nice modern detectors,
that the weaklings are underestimated?
Do I really want to inflate them?
Exactly what assumptions is it making about the expected
distributions?
How compatible are those assumptions with serious anisotropy
and the wierd Wilson plots that nucleic acids give?
Note the original 1978 French and Wilson paper says:
"It is nevertheless important to validate this agreement for
each set of data independently, as the presence of atoms in
special positions or the existence of noncrystallographic
elements of symmetry (or pseudosymmetry) may abrogate the
application of these prior beliefs for some crystal
structures."
Please help truncate my ignorance ...
Phoebe
==========================================================
Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry & Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123
RNA is really nifty
DNA is over fifty
We have put them
both in one book
Please do take a
really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp
