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-----
