Note that Scala & Aimless always put I+, I- and Imean into the output file, which then get propagated through [c]truncate. This is irrespective of whether the Anomalous data flag is switched on: that only affects outlier rejection and some statistics. Note also that Aimless (recent versions anyway) will automatically switch on the Anomalous flag if there appears to be a significant anomalous signal, unless you explicitly tell it not to (to avoid accidentally rejecting good anomalous differences as outliers)
Phil
On 5 Dec 2012, at 09:35, Tim Gruene wrote:
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> If you don't want scala to keep your Bijvoet-pairs separate, you
> should uncheck the appropriate button in the ccp4i-GUI. However, since
> you have SIGF_New, your mtz-file already contains the merged
> Bijvoet-pairs.
>
> Scala is not a refinement programm and you ought to check the input
> file for phenix where to tell it to use the merged data rather than
> the unmerged data, and also need to check the phenix log-file to
> figure out why it calculates the completeness so low.
>
> Regards,
> Tim
>
> On 12/04/2012 11:55 PM, Yarrow Madrona wrote:
>> Hello CCP4 users,
>>
>> My column labels from scala include:
>>
>> SIGF_New(+) and F_New as well as F_New(-) and SIGF_new(-)
>>
>> But also contains: SIGF_New, F_New DANO_New and SIGDANOW_NEW
>>
>> When I refine (phenix) using SIGF_NEW(+) and SIGF_New(-) my
>> completeness does not match what comes out of the scala log file
>> (97%). Instead it is only 90%
>>
>> But when I refine using Intensities and let phenix.refine run
>> truncate I get the expected completeness of 97% in my log file.
>>
>> Is there something special you have to do in Scala to tell it to
>> combine anomalous and non-anomalous data for refinement using
>> structure factors?
>>
>> I don't need the anomalous data so I don't need to keep it
>> separate.
>>
>> Thanks.
>>
>> -Yarrow
>>
>>
>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
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