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: [log in to unmask]
>> *******************************************
>> ----- Original Message ----- From: "Bart Hazes" <[log in to unmask]
>> >
>> To: <[log in to unmask]>
>> 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
>
> =
> =
> =
> =
> =
> =
> =
> =
> ======================================================================
|