Re: [phenixbb] Anomalous or not?

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 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:

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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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