Surely Refmac or any other program should honour the symmetry operators in the MTZ file - that's why they are there!
Phil
On 23 May 2014, at 12:34, Eleanor Dodson <[log in to unmask]> wrote:
>
> Someone here has seen his Rfactors leap from 18% to 42% and was naturally distressed!
> We have tracked down the problem to this:
>
> Steps he took were:
>
> 1) Integrate with XDS and feed output through pointless/aimless etc.
> He used a phenix refined mtz to "Match Laue and indexing"
>
> The space group there is given by PHENIX
> as "P 2 21 21 " but the spacegroup NUMBER is given as 18 (ie P21 21 2 in CCP4 symmetry library) .
>
> pointless then output an mtz file with SPACEGROUP number as 18 and SG name as P 2 21 21.
> The symmetry operators are correctly listed for P 2 21 21
> This is the version number: CCP4 6.4: POINTLESS version 1.9.8 : 02/05/14
>
> 2) When the refinement was repeated with REFMAC the spacegroup was taken as P21 21 2 - ie the SG number 18 overrode the listed symmetry operators in the mtz file, and the SG name P 2 21 21 given on the CRYST1 card was ignored.
>
> The refmac version used is CCP4 6.4: Refmac_5.8.0071 version 5.8.0071 : 04/04/14
>
>
> The user thinks that in REFMAC 5.8.0033 this problem did not occur, but I havent checked that..
>
>
> Anyway - it does emphasise the importance of checking symmetry operators for consistency with both the SG name and number (Yes, George, I know you have always said this is the only correct policy!) Maybe an extra subroutine could be added to the symmetry library and called from other programs..
>
> And ideally checking all sources of symmetry information for consistency and stopping if there is a serious disagreement.
>
>
> In the short term we simply took the processed mtz file and ran
> mtzutils hklin1 corrupted.mtz hklout fixed.mtz
> SYMM 3018 (or symm "P2 21 21" )
> and the fixed file was OK
>
> Eleanor Dodson
>
>
>
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