Hi, Space group is P21, cell parameters is 40.29 66.01 161.37 90.00 94.09 90.00
From Aimless: ------------------------------------------------------------------------------------------------ | operator | L-test | |Rtwin| | H-test | Britton | ML Britton | ------------------------------------------------------------------------------------------------- | -h, -k, h+l | Yes | 0.34 | 0.14 | 0.11 | 0.05 ( N/A ) | ------------------------------------------------------------------------------------------------- From refmac: Twin operator: H, K, L : Fraction = 0.806; Equivalent operators: -H, K, -L Twin operator: H, -K, -H-L: Fraction = 0.194; Equivalent operators: -H, -K, H+L In viewhkl summary all columns go to 2.0 Å. Robert _______________ Robert Gustafsson PhD Student Department of Biochemistry and Biophysics Stockholm University 106 91 Stockholm, Sweden e-mail: [email protected] <mailto:[email protected]> > On 21 Oct 2016, at 11:54, Eleanor Dodson <[email protected]> wrote: > > Hmm - what is your space group, cell, and twin law? > The mtz file output from REFMAC contains detwinned data - ie the column > labelled as F is NOT the measured amplitude derived from the measured twinned > intensities. > > So in some SGs it is conceivable that an index has been generated.. > This shouldnt happen with merohedral twinning but it can with > pseudo-merohedral twinning. > > No the other hand, are you sure the extended resolution does not just involve > the Free R column? look at the viewhkl summary to see if all columns extend > to 2.0 resolution > Eleanor > > > > On 21 October 2016 at 09:24, Robert Gustafsson <[email protected] > <mailto:[email protected]>> wrote: > Hi all, > > I am currently refining a structure that is at a resolution of 2.1Å and > slightly twinned. Below is the message in the aimless results: > > WARNING: the L-test suggests that the data may be twinned, so the indicated > Laue symmetry may be too high > Rough estimated twin fraction alpha from cumulative N(|L|) plot 0.209 > +/-(0.015) > Rough estimated twin fraction alpha from < |L| > 0.202 > Rough estimated twin fraction alpha from < L^2 > 0.192 > > I have been refining with twin refinement, and without, and using twin > refinement gives better R-factors, as expected. > > When looking in the results files more carefully however, it seems that 0.1Å > of data have been added to my data in the detwinning process! It suddenly > comes out of refmac with a 2.0 Å in both pdb and mtz resolution, and it just > suddenly seems to decide that for itself. I have looked for differences in my > input and there is none other than choosing amplitude or intensity based twin > refinement, instead of no twin refinement. Input mtz and pdb are the same, > but in the log file of refmac it suddenly uses 2.0 Å. > > This error is not captured afterwards, both Molprobity and PDBe validation > tool finds the structure to now be 2.0Å resolution, however i can see in both > refmac output and PDBe validation output that the completeness is lowered > (which I guess would be expected since some data does not exist…) > > So the question is, is this a bug of some sort, or should I have chosen > something in the input of refmac? I am using the latest update of ccp4 > (7.0.021) using the CCP4i interface. I have looked back at my files ( the > project started 2 years ago) and the problem was there as well, so it is not > a new problem. > > Sincerely, > Robert Gustafsson > > > _______________ > Robert Gustafsson > PhD Student > Department of Biochemistry and Biophysics > Stockholm University > 106 91 Stockholm, Sweden > > e-mail: [email protected] <mailto:[email protected]> > > >
