Oh dear - you should always start refinement against the original processed data - but others have told you that already..
The TLS files will not be appropriate for the rescaled FPs - it is surprising that the Rfactor actually goes down though! Or are you doing several cycles of refinement in thesecond pass too - in that case one would hope the Rfactor would continue to fall. Eleanor On 17 July 2013 11:00, Guenter Fritz <guenter.fr...@uni-konstanz.de> wrote: > Am 17.07.2013 11:59, schrieb Guenter Fritz: > >> Hi Stefan and Gottfried, >> thanks a lot for the answers. This is the point. Wouldn't it make more >> sense to add an extra column that contains the changed Fs? >> Best, Guenter >> >> Hi, >>> >>> it is strongly advised to use the original mtz e.g. scala.mtz as the >>> refmac input mtz in all refmac runs, >>> as this contains the original Fs - Refmac applies some aniso corrections >>> to the Fs and puts them into the output.mtz. >>> >>> so the output Fs are not the same as in the input F - therefore one >>> should use the scala.mtz >>> >>> cheers >>> Stefan >>> >>> >>> -----Ursprüngliche Nachricht----- >>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von >>> Guenter Fritz >>> Gesendet: Mittwoch, 17. Juli 2013 10:39 >>> An: CCP4BB@JISCMAIL.AC.UK >>> Betreff: [ccp4bb] TLS refinement refmac >>> >>> >>> Dear all, >>> >>> one gets different R values, if you re-read in the mtz written out by >>> refmac after TLS refinement. I think this issue had been a while ago in >>> ccp4bb, but I can't find the right track. >>> >>> Here are the details. >>> >>> 1st run: >>> If we do TLS + restr. refinement in refmac we get: >>> Initial Final >>> R factor 0.3010 0.2170 >>> R free 0.3175 0.2695 >>> >>> 2nd run: >>> Now, if we use the same input pdb and the same input tls paramter file, >>> but use the mtz written out by the first run, we get: >>> Initial Final >>> R factor 0.2274 0.1903 >>> R free 0.2482 0.2540 >>> >>> >>> Apparently in the mtz file written out by the 1st refmac must contain >>> some information that is re-read in the 2nd run. But one just defines >>> FP, SIGFP and Rfree flags. Do FPs change in the output mtz after TLS >>> refinement?? >>> >>> Any help to clarify this is appreciated. >>> >>> Thanks, Guenter >>> >> >>
