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 <http://www.ccp4.ac.uk/html/almn.html>), or by keyword POLAR followed by polar angles omega, phi, kappa (as in POLARRFN <http://www.ccp4.ac.uk/html/polarrfn.html>). This transformation will be applied to all atoms. The SHIFT <http://www.ccp4.ac.uk/html/pdbset.html#shift> command may be used to define a translation in addition. The transformation defined by ROTATE & SHIFT, or by TRANSFORM <http://www.ccp4.ac.uk/html/pdbset.html#transform>, is applied after any SYMGEN <http://www.ccp4.ac.uk/html/pdbset.html#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 > <https://maps.google.com/?q=71+avenue+des+Martyrs&entry=gmail&source=g> > 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 > <http://www.ibs.fr/research/research-groups/viral-replication-machines-group-m-jamin/team-03/article/poxvirus-replication-machinery-presentation/> > map > <https://www.openstreetmap.org/?mlat=45.20762&mlon=5.69255#map=17/45.20762/5.69255> > > >
