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That is interesting - we often (well, fairly often) get Is labelled as Fs or vice versa in files downloaded from thr PDB - this can be detected from intensity stats and maybe there should be a default warning! Eleanor On 20 April 2016 at 13:26, Randy Read <[log in to unmask]> wrote: > Dear Sam, > > Thanks for sorting that out! > > Best wishes, > > Randy > > On 20 Apr 2016, at 13:06, Sam Tang <[log in to unmask]> wrote: > > Dear Professor Read and colleagues > > Thanks for your kind attention to the question. On closer look into the > log file and the parameters, it happened to be that our project student > mis-set IMEAN and SIGIMEAN to F and SIGF which mis-led the programme in > tNCS correction. The run seems normal when we rectify this silly mistake > (on which we've spent two whole afternoons trying to look out why!) > > Sorry for all the inconvenience. > > Kind regards > > Sam > > PhD candidate > Biochemistry Programme, School of Life Sciences, CUHK > > > On 20 April 2016 at 16:33, Randy Read <[log in to unmask]> wrote: > >> Dear Sam, >> >> As far as I know, changing the sequence identity or the number of copies >> of the model shouldn't have any effect on the moments calculations in >> Phaser. Changing the number of copies could change other things >> downstream. For instance, if translational NCS (tNCS) is detected but the >> number of copies you are searching for is not divisible by the number of >> copies related by tNCS, the tNCS correction is not applied in the >> calculation. Nonetheless, even then, the tNCS analysis is used in the >> moments calculations. >> >> Could you send me the two complete log files (preferably offline) so I >> can see what has happened here? >> >> Thanks! >> >> Best wishes, >> >> Randy Read >> >> > On 19 Apr 2016, at 12:32, Sam Tang <[log in to unmask]> wrote: >> > >> > Hello, >> > >> > I am carrying out molecular replacement on one of our recent data set >> using Phaser-MR. The data set was indexed P1 to 2.5 Angstorm. In my initial >> run, Phaser-MR returned the following: >> > >> > -------- >> > TWINNING >> > -------- >> > >> > tNCS/Twin Detection Table >> > ------------------------- >> > -Second Moments- >> --P-values-- >> > Centric Acentric untwinned twin >> frac <5% >> > Theoretical for untwinned 3.00 2.00 >> > Theoretical for perfect twin 2.00 1.50 >> > Initial (data as input) 0.00 2.41+/-0.070 1 1 >> > After Anisotropy Correction 0.00 2.12+/-0.052 1 1 >> > After Anisotropy and tNCS ---n/a--- >> > >> > P-value < 0.01 for <5% twinned is considered significant >> > Resolution for Twin Analysis (85% I/SIGI > 3): 3.54A (HiRes= 2.67A) >> > >> > >> > Afterward the initial run I tried to re-run the job keeping all input >> mtz and model pdb and other parameters the same. (I simply click 'ReRun >> job' on the menu.) The only adjustments were (1) ensemble IDENT from 90% to >> 95%; (2) No. of copies to search for from 2 to 1. This time the programme >> warns of significant twinning: >> > >> > >> > -------- >> > TWINNING >> > -------- >> > >> > tNCS/Twin Detection Table >> > ------------------------- >> > -Second Moments- >> --P-values-- >> > Centric Acentric untwinned twin >> frac <5% >> > Theoretical for untwinned 3.00 2.00 >> > Theoretical for perfect twin 2.00 1.50 >> > Initial (data as input) 0.00 1.35+/-0.013 0 0 >> > After Anisotropy Correction 0.00 1.29+/-0.011 0 0 >> > After Anisotropy and tNCS ---n/a--- >> > >> > P-value < 0.01 for <5% twinned is considered significant >> > Resolution for Twin Analysis (85% I/SIGI > 3): 3.15A (HiRes= 2.67A) >> > >> > >> ------------------------------------------------------------------------------------- >> > Warning: Intensity moments suggest significant twinning (>5%). Tests >> based on >> > possible twin laws will be more definitive. >> > >> ------------------------------------------------------------------------------------- >> > >> > >> > To my understanding Phaser first treats the data for twin / not twin >> before it really puts in the model. Thus I am curious why the same set of >> input data and model give different results in Twinning test? >> > >> > Thanks! >> > >> > Sam >> > >> > PhD Candidate, The Chinese University of Hong Kong >> >> ------ >> 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: [log in to unmask] >> Cambridge CB2 0XY, U.K. >> www-structmed.cimr.cam.ac.uk >> >> > > ------ > 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: [log in to unmask] > Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk > >