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 >> >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v1.4.12 (GNU/Linux) >> Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ >> >> iD8DBQFQvxVjUxlJ7aRr7hoRAgyeAJ4t8V7H9aDfzuf1lqT3RzULYmSSRQCg8Bj+ >> zgcEB/KN7LIVONVPcIz0nFg= >> =fL/K >> -----END PGP SIGNATURE----- > > -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697
