*** For details on how to be removed from this list visit the ***
*** CCP4 home page http://www.ccp4.ac.uk ***
Dear Yi,
Yup- looks like no signal-
but be careful. There is something peculiar about this test as described
in the manual. Just using the "anomalous" flag does not cause Bivoet mates
to be treated separately- they are still considered equivalent in scaling and
calculating the statistics.
So if you had chi^2 about one scaling all the data with the anomalous flag,
with Bivoet mates considered equivalent (but output separately), and you still
had chi^2 about one when you rescale that dataset with Bivoet mates considered
equivalent, that doesn't really prove there is no signal (I think).
The manual does not say to compare chi^2 in the first and second scaling-
just that the value of chi^2 in the second round should be greater than 1.
Last paragraph: "This whole analysis assumes the error model is reasonable and
gives chi^2 close to one when the 'Scale Anomalous' flag is used". ('scale
anomalous' unlike 'anomalous' causes bivoet mates to be treated as
non-equivalent in scaling and calculating statistics).
The test you really want to do is to use 'scale anomalous' in the first round,
but the author seems to fear your anomalous data is not complete enough for
scale anomalous to work well. Give it a try, anyway!
<If I completely misinterpreted this strategy, please someone
chime in to correct me>
Others could better answer your final questions, but for my 2 cents:
The R values look fine, even considering redundancy is only 2 in the
second scaling.
Chi^2 is a standard statistical parameter, something like the ratio of
the obsered deviations from the mean to those expected based on your error
model. This takes into consideration the decreased redundancy with "scale
anomalous", which would improve the R-factors even in the absence of an
anomalous signal.
If your error model were correct, and there is an anomalous signal,
you should get chi^2 > 1 with or without the anomalous flag, and
close to one with "scale anomalous" as the author indicated.
Ed
Yi Xue wrote:
Hi, all:
I collected Cu-MAD data, I tried to detect anomalous signals using
scalepack.
I followed tutorial: first: scale data with 'anomalous' checked, and chi
square around 1.
second: turn off 'anomalous' flag, and merge I+ and
I-.
Output is as follows:
===========================================snip==============================
____________________________________________________________________________
_____
I am confused by Chi square and R factor values. It seems that at higher
resolution, R factor is very high, does it mean there is a big difference
between I+ and I-? Is it caused by synchrotron radiation damage? Besides,
what are the ideal values for R factors, should they be constant throughout
all resolution shells?
Meanwhile, Chi square values are mostly around 1, which should be indicative
of no anomalous signal. Where does chi square derive from? and, what is the
real meaning of it?
thank you very much
Yi
