[phenixbb] Anomalous or not?

Tim Gruene tg at shelx.uni-ac.gwdg.de
Thu Jul 10 06:22:57 PDT 2014

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running auto-whatever- when you are dealing with critical data is
usually not the way to get the best results. Experience with parameter
settings is usually more powerful then generalised default settings.

Reading the documentation of autoxds, there is an important caveat,
where autoxds might corrupt your anomalous signal:

The CORRECT step scales your data. It appears that autoxds will call
aimless or scala to scale your data again. This is little harmful for
the intensities, but corrupts the sigma values because the error model
is applied twice and thus it is harmful for phasing using the
anomalous signal because this relies on proper sigma values.

At the CCP4 workshop in Chicago Garib Murshudov pointed out that when
your CC(1/2) is 40% in the outer resolution shell (or CC*(1/2) = 50%)
AND I/sigma is approximately 1.0, your sigma values are probably
correct (this may be mentioned in the Karplus/Diederichs paper and
attributed accordingly). I found this the most useful rule of thumb so
far to decide about the resolution cut-off.


On 07/10/2014 03:13 PM, Tim Gruene wrote:
> Dear Charles Chen,
> I am not familiar with autoxds, only xds itself. The reported
> quality of the anomalous signal is quite reliably and consistent
> with that of other programs, although the resolution shells listed
> in CORRECT.LP are a little broad, why I prefer to run xscale and
> take a look at XSCALE.LP (which would also combine your data by the
> way).
> I would recomment NOT to set FRIEDEL'S_LAW=FALSE in XDS, especially
> if you only have weak anomalous signal. The small differences in
> the Bijvoet pairs does not really affect the scaling, but the
> doubled number of reflections gives you much more reliable scaling
> so that you end up with a stronger anomalous signal with
> Regards, Tim
> On 07/10/2014 03:03 PM, CPMAS Chen wrote:
>> Hi, Phenix Users,
>> I recently collected data at SSRL. I used autoxds and multiscale
>> to merge couple of datasets and hoped to see some anomalous
>> signals. Now comes the questions.
>> 1. if I use the default sigma(=2), then autoxds will report weak 
>> anomalous signals and leave the friedel flag off. If I lower
>> sigma to 1.5, it will report strong anomalous signals. 2. when I
>> used Xtriage under Phenix to check the data quality, it reported
>> weak anomalous signal or at above 10A. 3. I used aimless (in
>> CCP4) to merge data, it also reported weak anomalous signal.
>> Which result should I trust? By the way, how can I view/display 
>> the ***.anamplot file, which is apparently xmgr format file, but
>> I can not display in CCP4i.
>> Thanks!
>> _______________________________________________ phenixbb mailing 
>> list phenixbb at phenix-online.org 
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- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen


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