-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 P.S.: 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. Cheers, Tim 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 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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- -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFTvpOxUxlJ7aRr7hoRAm5HAKDoMjGCRgwy4zP77z6bs5dL0sb9LwCcDN1D Kjh1UPy5LVcnQVg4rXlif6c= =WUoO -----END PGP SIGNATURE-----