[phenixbb] Anomalous or not?

[Tim Gruene]

Hi Phil,

I had borderline cases in mind where you are at the limit of
solvability. In such a case you want to get the best out of your data as
possible and avoid any harm when possible. And since you never know if a
case is borderline until it is solved, I think it is good practice to do
it right anyway.

My comments are based on experience from Kay and George, who have done a
few tests on phasing with shelxd.

I agree that the changes are small.

Best,
Tim

On 07/10/2014 04:52 PM, Phil Evans wrote:
> 
> I don't think the sigma analysis/correction twice should mess things up too much - there will be some differences but the 2nd "correction" probably won't do much if it thinks the 1st correction has done the job (i.e. it shouldn't hurt)
> 
> Phil
> 
> On 10 Jul 2014, at 14:13, Tim Gruene <tg at shelx.uni-ac.gwdg.de> 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 FRIEDEL'S_LAW=TRUE.
> 
> 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!
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
> 
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-- 
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

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