Re: [ccp4bb] Scale datasets from different crystals

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Is my data twinned or not?
From: "Garnett, James A" j {- dot -} garnett {- at -} IMPERIAL {- dot -} AC {- dot -} UK
Date: 2009-09-02

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Subject: Protein Crystallography course via the web at Birkbeck College
From: Tracey Barrett t {- dot -} barrett {- at -} MAIL {- dot -} CRYST {- dot -} BBK {- dot -} AC {- dot -} UK
Date: 2009-09-02

Subject: Re: Scale datasets from different crystals
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-09-02

These are just warnings: Scala will combine them & average the unit
cells

Phil

On 18 Aug 2009, at 13:10, Donald Damian Raymond wrote:

> I tried to scale the two datasets in scala after combining the two
> unmerged datasets with the sort MTZ program, but scala thinks the
> two datasets are from the same crystal. The problem is the unit cell
> constants are not identical. See scala output below.
>
> * Number of Datasets = 2
>
> * Dataset ID, project/crystal/dataset names, cell dimensions,
> wavelength:
>
> 1 0409
> 0409
> JL0409
> 66.7900 69.4500 80.4500 83.1500 70.4700 61.5600
> 0.97952
> 2 0609
> 0409
> JL0409
> 66.9700 69.5600 80.4500 83.0600 70.6700 61.2900
> 1.03319
>
> Then I get this WARNING:
>
> WARNING: output dataset X101/two/JL0609 contains input datasets with
> different wavelengths
>
> WARNING: output dataset X101/two/JL0609 contains input datasets with
> different cells
>
> WARNING: output dataset X101/two/JL0609 contains input datasets with
> different Crystal Names
>
> clearly scala is expecting data from the same crystal. Are there any
> programs in ccp4 that I can use to combine these two datasets. I
> know this sort of thing was done a lot before cryoprotection came
> about. Thanks a lot in advance.
>
> -Donald
> ---------------------
> Donald Raymond
> Department of Biological Chemistry
> Janet Smith Lab
> University of Michigan
>
>
> On Aug 17, 2009, at 10:34 PM, Pete Meyer wrote:
>
>> If you want to treat the end result as a single dataset, you're
>> probably better off combining unmerged datasets (two different
>> batches in scala, or two different scaling sets in scalepack).
>>
>> As far as I understand it, the data model in the mtz files (project/
>> crystal/dataset/column) isn't really set up to allow combining two
>> datasets post-merging; so most likely you'd have to cook up a
>> custom procedure (most likely involving some duct tape, or
>> equivalently dumping to ascii after scaling, merging overlapping
>> reflections, and reconversion to mtz).
>>
>> Pete
>>
>> Donald Damian Raymond wrote:
>>> Hello all,
>>> I have incomplete data from two different crystals. Is there a
>>> program in ccp4 that I can use to merge the two scaled datasets?
>>> I used CAD and scaleit, but it does not give any scaling
>>> statistics like completeness and Rmerge. Any help would be
>>> appreciated.
>>> -Donald.
>>
>>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Is my data twinned or not?
From: "Garnett, James A" j {- dot -} garnett {- at -} IMPERIAL {- dot -} AC {- dot -} UK
Date: 2009-09-02