Scala has an option (ANOMALOUS MATCH INRUN) to select "matching"
Bijvoet pairs, which will have a similar effect to average DelAnom,
but when I've tried it, it has given worse results than just chucking
everything in together
Phil
On 23 Jul 2008, at 16:53, Bart Hazes wrote:
Jacob Keller wrote:
Shouldn't all of the "crystal-to-crystal" differences be taken out
automatically by scaling,
Scaling only takes out differences in overall scale, B-factor and,
if you have enough data, it can correct to some extend for
absorption or other more local effects. Systematic differences due
to slight differences in unit cell, molecular packing etc lead to
different relative intensities that are not removed by scaling.
and is there not the same proportional anomalous signal in every
isomorphous crystal, regardless of the background? I would think
that using multiple crystals would give a better idea of "the
truth," as if taking many snapshots of the same object, and putting
them together to form a three-dimensional object. In Hazes'
language, don't all isomorphous crystals "draw from the same
[underlying] distribution?"
The answer is yes when the crystals are truly isomorphous. In
reality they rarely if ever are. The differences tend to be small
enough that you normally don't have to worry about it for heavy atom
derivatives or native data sets. However, for weak anomalous signals
it is a different story.
Bart
Jacob Keller
ps admittedly if there is radiation damage or other non-
isomorphisms, this reasoning does not apply.
*******************************************
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: [EMAIL PROTECTED]
*******************************************
----- Original Message ----- From: "Bart Hazes" <[EMAIL PROTECTED]
>
To: <CCP4BB@JISCMAIL.AC.UK>
Sent: Wednesday, July 23, 2008 10:05 AM
Subject: Re: [ccp4bb] Using multiple crystals for structure
solution in P1 using MAD/SAS/SAD
Increasing redundancy only helps if all data draw from the same
distribution so you get a more accurate estimate of the mean of
the distribution. When dealing with different crystals, crystal-to-
crystal variation is likely larger than the anomalous signal you
are looking for and I'm therefore not convinced that merging of
data is a good idea (never hurts to try though).
I wonder if it would work better to derive anomalous differences
for the individual data sets first and then merge those anomalous
differences. This may allow the subtraction between F+ and F- to
remove some of the systematic differences there may be between
crystal forms.
Bart
Kay Diederichs wrote:
hari jayaram schrieb:
...
I was wondering if anyone could comment on combining datasets
from multiple P1 crystals to increase the redundancy even
further for such heavy atom ( SAS / SAD ) or MAD experiments.
Hari,
well, my comment would be that it should be possible in principle
from what you describe, but the outcome strongly depends on the
details (size of expected and observed anomalous and isomorphous
signal, internal anomalous correlation coefficients, I/sigma and
R-factors, radiation damage, are crystals isomorphous, ...).
To increase the quality of the reduced data it would be advisable
to rotate around different axes, which is possible at some - but
not all - beamlines. This is even more true in P1.
For all of the major data reduction programs there exist specific
programs for merging data, and it does make a lot of sense to
merge your passes (but don't merge radiation-damaged data with
undamaged data)!. I would suggest to use at least two different
data reduction packages - everything depends on the quality of
the data reduction, and the programs have strengths in different
areas.
HTH,
Kay
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Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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Bart Hazes (Assistant Professor)
Dept. of Medical Microbiology & Immunology
University of Alberta
1-15 Medical Sciences Building
Edmonton, Alberta
Canada, T6G 2H7
phone: 1-780-492-0042
fax: 1-780-492-7521
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