If you can transform the coordinates correctly, then Pointless can transform the data to match, using the coordinates as reference

pointless <<EOF hklin input.mtz hklout output.mtz xyzin reference-coordinates.pdb EOF If you have transformed the reflections, then the easiest thing to do is to run a (trivial) molecular replacement (saves thought :-)) Phil > On 17 May 2018, at 12:39, Eleanor Dodson > <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Yes - here is a bit of the output from reindexing a set of H32 data to C2 > > It tells you this and issues some warnings! > > > > !!!! You are changing the symmetry of merged data are you SURE you know > what you are doing!!!! > > <B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN--> > > $TEXT:Warning: $$ comment $$ > WARNING: ** Symmetry change of merged data ** > $$ > <!--SUMMARY_END--></FONT></B> > > New unit cell determined from reindexing: 163.50 136.44 106.47 90.00 > 103.48 90.00 > > > > > Data line--- symmetry C2 > Data line--- reindex HKL -h/3 -2k/3 -2l/3, h, -h/3-2k/3+l/3 > Data line--- noreduce > Data line--- end > > Reflections will be reindexed, and unit cell recalculated > > Reindexing transformation: > (h' k' l') = ( h k l ) ( -0.33333 1.00000 -0.33333 ) > ( -0.66667 0.00000 -0.66667 ) > ( -0.66667 0.00000 0.33333 ) > > > > Real axes transformed by same matrix: > (a' b' c') = ( a b c ) ( -0.33333 1.00000 -0.33333 ) > ( -0.66667 0.00000 -0.66667 ) > ( -0.66667 0.00000 0.33333 ) > > > > Reciprocal axes transformed by inverse matrix: > (a*') ( 0.00000 -0.50000 -1.00000 ) ( a*) > (b*') = ( 1.00000 -0.50000 0.00000 ) ( b*) > (c*') ( 0.00000 -1.00000 1.00000 ) ( c*) > > > FRACTIONAL coordinates transformed by same matrix: > (x') ( 0.00000 -0.50000 -1.00000 ) ( x) > (y') = ( 1.00000 -0.50000 0.00000 ) ( y) > (z') ( 0.00000 -1.00000 1.00000 ) ( z) > > > On 16 May 2018 at 22:20, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > Of course you need to give pdbset the new cell too... > E > > On 16 May 2018 at 22:20, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: > Hmm - I think you need > pdbset > symgen x-y/2,y/2,z > > Dont have reindex output at home but doesnt it tell you > [h' k' l'] = [h k l ] [ 1 1 0] > [ 0 2 0] > [ 0 0 1] > > [a* ' ] . [ 1. -1/2. 0]. [a*] > [b* ']. =. [ 0 1/2 0]. [b*] > [c* ']. [ 0. 0 1] [c*] > > [a' b' c'] = [a b c ] [ 1 1 0] > [ 0 2 0] > [ 0 0 1] > > [x '] [ 1. -1/2. 0]. [x] > [y ']. =. [ 0 1/2 0]. [y] > [z ']. [ 0. 0 1] [z] > > > Cheers Eleanor > > > > > On 16 May 2018 at 01:11, James Holton <jmhol...@slac.stanford.edu> wrote: > > Wow, really? I thought all reindex gives us is the axis transformation, not > the coordinate transform. > > I just tried going from P622 into C222, starting with 3hjd. By using > othercell, I can get an operator for transforming the data: h,h+2k,l. > Applying this in reindex, I get the matrix: > > Real axes transformed by same matrix: > (a' b' c') = ( a b c ) ( 1.00000 1.00000 0.00000 ) > ( 0.00000 2.00000 0.00000 ) > ( 0.00000 0.00000 1.00000 ) > But if I apply: > > pdbset xyzin 3hjd.pdb xyzout test.pdb << EOF > symgen X,X+Y+Y,Z > EOF > I get some rather significant geometric distortions. > > Am I doing something wrong? Or is this just harder than it seems? > I find it is a common problem my users face. They can get an MR solution if > they over-merge their data, but not when it is merged in any other space > group. The transition from the P622 to C222 is the most thorny one. > Twinning in C222 can get you to apparent P622, and I wonder if ignorance of > how to transform the coordinates is the reason why there are no examples of > this in the PDB. > > Thanks in advance for your always-appreciated insight! > > -James > > > > On 5/15/2018 3:15 AM, Eleanor Dodson wrote: >> Well - if you use reindex to change the reflections from I213 to P1 the log >> file gives the rotation matrix need to convert I213 coordinates using the >> same convention. >> There are various clever inputs to reindex which allow you to do this >> >> Then you can use >> >> pdbset xyzin I213.pdb xyzout P1.pdb giving that matrix. >> From the doc.. >> >> ROTATE [INVERT] [MATRIX|EULER|POLAR] values >> >> Define rotational transformation, either as MATRIX (this keyword may be >> omitted) followed by 9 numbers (r11 r12 r13 r21 r22 r23 r31 r32 r33), by >> keyword EULER followed by Eulerian angles alpha, beta, gamma (as in ALMN), >> or by keyword POLAR followed by polar angles omega, phi, kappa (as in >> POLARRFN). This transformation will be applied to all atoms. The SHIFT >> command may be used to define a translation in addition. The transformation >> defined by ROTATE & SHIFT, or by TRANSFORM, is applied after any SYMGEN >> operation. Multiple definitions of ROTATE or TRANSFORM, or of SHIFT will NOT >> be concatenated: only the last will be effective. >> >> Eleanor >> >> >> On 15 May 2018 at 09:51, Wim Burmeister <wim.burmeis...@ibs.fr> wrote: >> Hello, >> does anybody have a script which transforms the pdb file of a structure in >> I-centred I213 into a pdb file based on the corresponding primitive P1 unit >> cell ? A rotation matrix would also do which uses the matrix of the >> transformation from one coordinate system to the other combined with the >> orthogonalisation convention for the P1 cell. >> Best >> Wim >> -- >> Wim Burmeister >> Professeur >> Institut de Biologie Structurale (IBS) CIBB >> 71 avenue des Martyrs >> CS 20192 >> 38044 Grenoble Cedex 9, FRANCE >> E-mail: wim.burmeis...@ibs.fr >> Tel: +33 (0) 457 42 87 41 Fax: +33 (0) 476 20 94 00 >> website >> map >> >> >> > > > >