On Wed, Aug 8, 2012 at 11:19 AM, Pavel Afonine wrote:

<Fobs> or "F/SigF and DF/SigDF" are derived from Fobs(+) and Fobs(-) with some information lost. That is you cannot restore the original Fobs(+) and Fobs(-) from <Fobs> or from "F/SigF and DF/SigDF". phenix.refine restores Fobs(+) and Fobs(-) from "F/SigF and DF/SigDF" for internal use making an arbitrary decision about the sign. phenix.refine cannot handle "F/SigF and DF/SigDF" and has no reason to do this.

Does XDS (or xdsconv) not include the ISYM column? In some files, we get a combination of columns like this: F SIGF DANO SIGDANO ISYM which is the same thing, but the ISYM column indicates how the DANO is applied to the Friedel mates, meaning that we can reconstruct the original F+ and F-. There's nothing wrong with using these data in Phenix - without ISYM, however, the DANO is useless. -Nat

Dear all, Thanks very much for the answers!!! Indeed I missed to include in my message that xdsconv outputs not only h,k,l,F,SigF,DF,SigDF, but also the isym,i - Im sorry. isym=0: both F(+) and F(-) were observed. F=(F(+) + F(-))/2; DF=F(+) - F(-) isym=1: only F(+) was observed. F=F(+); DF and SigDF are omitted from the output record. isym=2: only F(-) was observed. F=F(-); DF and SigDF are omitted from the output record. So it seems to be OK. Since I refine directly SAD data i find convenient to have also the DF/SigDF in order to make anomalous difference maps if needed. Its just ive never seen a pdb header with this "doubled" test set count column. Maybe most of the people use only averaged data (<F> <SigF>) for refinement whatever the data (SAD or Native). Thanks a lot once again! All best Filip On 2012-08-08 20:34, Pavel Afonine wrote:

I've seen files with bare F SIGF DANO SIGDANO. Not sure what Filip has. Yes, if instructions about how to reconstitute +/- reflections are provided then that all right.

Pavel

On 8/8/12 11:26 AM, Nathaniel Echols wrote:

...

On Wed, Aug 8, 2012 at 11:19 AM, Pavel Afonine wrote:

...

<Fobs> or "F/SigF and DF/SigDF" are derived from Fobs(+) and Fobs(-) with some information lost. That is you cannot restore the original Fobs(+) and Fobs(-) from <Fobs> or from "F/SigF and DF/SigDF". phenix.refine restores Fobs(+) and Fobs(-) from "F/SigF and DF/SigDF" for internal use making an arbitrary decision about the sign. phenix.refine cannot handle "F/SigF and DF/SigDF" and has no reason to do this. Does XDS (or xdsconv) not include the ISYM column? In some files, we get a combination of columns like this:

F SIGF DANO SIGDANO ISYM

which is the same thing, but the ISYM column indicates how the DANO is applied to the Friedel mates, meaning that we can reconstruct the original F+ and F-. There's nothing wrong with using these data in Phenix - without ISYM, however, the DANO is useless.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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