Thanks to everyone for their input.
Yes, it appears that F_new from scala includes the anomalous data.
Something weird is going on when I use these labels vs. Intensity. In
refinement when I use intensity, phenix.refine does a french & wilson
method which is also done in truncate and I get the full completeness. I
do not now why I do not get the full completeness from the structure
factor conversion from Scala's truncate. I have tried to eliminate my own
errors but is likely something I have done wrong.
For now I will use phenix.refine to convert to structure factors. Thanks
for all of your input.
-Yarrow
> 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:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
>> Hash: SHA1
>>
>> 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
>>
>> GPG Key ID = A46BEE1A
>>
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>> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
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>
>
--
Yarrow Madrona
Graduate Student
Molecular Biology and Biochemistry Dept.
University of California, Irvine
Natural Sciences I, Rm 2403
Irvine, CA 92697
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