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Subject:

Re: Script / matrix for coordinate transformation from a cubic I cell to its primitive P cell ?

From:

Phil Evans <[log in to unmask]>

Reply-To:

Phil Evans <[log in to unmask]>

Date:

Thu, 17 May 2018 13:08:47 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (165 lines)

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 <[log in to unmask]> 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 <[log in to unmask]> wrote:
> Of course you need to give pdbset the new cell too...
> E
> 
> On 16 May 2018 at 22:20, Eleanor Dodson <[log in to unmask]> 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 <[log in to unmask]> 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 <[log in to unmask]> 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: [log in to unmask]
>> Tel:    +33 (0) 457 42 87 41       Fax: +33 (0) 476 20 94 00
>> website
>> map
>> 
>> 
>> 
> 
> 
> 
> 

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