Old tools still work. mtzutils allows you to select a zone eg: only output reflections with h even and k even look at the documentation to select what you want.
Eleanor On 26 February 2013 10:03, Randy Read <[email protected]> wrote: > Hi, > > In your specific case, you can predict that reflections for which the l > index is a multiple of 9 will be particularly strong, while others will be > weaker. So you could use sftools to select reflections that are a multiple > of 9 and write them into one MTZ file. > > sftools > read my.mtz > select index l zone 9n > write my_stronger.mtz > stop > yes > > To get the rest of the reflections, you can add the "select invert" > command after the initial "select index…" command to get everything else. > > A more general way is to run a recent version of Phaser, choosing the NCS > mode. Presumably there are 9 copies related by the translational NCS. The > default in Phaser is to assume there are two copies related by tNCS, if > there's a large peak in the native Patterson, so you would have to tell it > there are 9 copies. Running from a script, you would use the command "TNCS > NMOL 9". The NCS mode produces an MTZ file containing a column labelled > NcsEps, which is the factor by which the tNCS increases the expected > intensity for each reflection. The log file has a histogram of NcsEps > values, so you could decide on a cutoff between weak and strong > reflections, then use sftools to select them. To get the reflections with > greater than average intensity, you could use something like this: > > sftools > read NCSanalysis.mtz > select column NcsEps > 1 > write bigeps.mtz > stop > yes > > I hope that helps! > > Randy Read > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > Wellcome Trust/MRC Building Fax: +44 1223 336827 > Hills Road > E-mail: [email protected] > Cambridge CB2 0XY, U.K. > www-structmed.cimr.cam.ac.uk > > On 26 Feb 2013, at 03:06, Yuan SHANG <[email protected]> wrote: > > > Dear all, > > currently, I have a data set scaled in P22121 which containing a PST > of (0.5,0.5,0.111). The structure were successfully solved by molecular > replacement. However, the R free factors remained as high as ~33% in the > refinement. I search the literature and found that it was common to have > such high R free factors in case of PST (Felix F.Vajdos,etc.,protein > science,1997;Arthur H.Robbins,etc.,Acta D,2010;Florence > Poy,etc,NSMB,2001;Cory L.Brooks etc,Acta D,2008;). In the 2001 NSMB > paper(doi:10.1038/nsb720), the authors split the dataset into 'weak,medium > and strong' reflections, and showed good refinement statistcs in the > 'medium reflection dataset'. Although I had good electron density maps to > show my solution is correct. To further convince the reviewers, I also want > to split my data set into such sub-datasets according to the symmetry. Did > anyone know how to split the data set in this case? > > > > Best regards, > > Yuan >
