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: <[email protected]>
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
--
==============================================================================
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
==============================================================================
--
==============================================================================
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
==============================================================================
