Hi James First off, welcome to CCP4BB!
I think a bit of matrix algebra solves your problem. Define for the original PDB file: Xf = SoXo (SCALE transformation orth -> fract). Xs = OoXo (ORIGX orth -> submitted) where upper case means matrix or vector, lower case (subscript) identifies different entities. Then for the transformed PDB file: Xt = TXo (orth -> transformed orth) Xf = StXt (transformed orth -> frac) Xs = OtXt (transformed orth -> submitted) To summarise we have: Xf = SoXo = StXt = StTXo Xs = OoXo = OtXt = OtTXo so finally we have: St = SoT^-1 Ot = OoT^-1 This gives the new SCALE & ORIGX matrices. Note that matrices will need to be homogeneous (4x4) if translations are involved! Sorry email (at least plain text email - HTML email would look a lot nicer) is not an ideal medium for matrix algebra! Unfortunately I can't promise that the graphics & other programs will treat the new SCALE & ORIGX records correctly - if not complain to the authors! Most likely is that they will simply ignore the SCALE & ORIGX records and display the transformed co-ordinates which then obviously won't be consistent with the crystallographic symmetry. HTH -- Ian On 13 March 2013 12:57, James Davidson <[email protected]> wrote: > Dear All,**** > > ** ** > > This is my first post to the group – so “Hello”! I have searched with not > much success to find an answer to my question, so I thought I would try > posting here for some expert advice.**** > > I should start by saying that I am not a crystallographer, but please > don’t hold that against me!**** > > ** ** > > I am working with PDB files that are being aligned to reference > structures, indirectly by (a) using the alignment tools in PyMOL, then (b) > extracting the transformation matrix and re-applying this to the ATOM / > HETATM entries outside of PyMOL (to avoid atom reordering / atom charging / > etc that occurs when directly exporting from PyMOL). Anyway, what I wanted > to know is is there a way that I could (or should?) reference that the PDB > file coordinates have been transformed? Is there a way of preserving the > ability of tools (eg PyMOL) to legitimately recreate the symmetry mates > from the transformed coordinates if I eg apply the same transform to some > of the data in CRYST1 and SCALE1, SCALE2, SCALE3? Or should I instead be > adding ORIGX1, ORIGX2, ORIGX3 entries to show that a transformation has > been applied? Or, indeed, should I just accept that my aligned coordinates > should no longer be expected to recreate the packing environment?**** > > ** ** > > I have read through what I think is the correct section of the PDB > documentation, but I must confess that my lack of expertise means I am in > danger of approaching an old(?) problem through naïve trial and error!**** > > ** ** > > Any help / advice greatly appreciated.**** > > ** ** > > Kind regards**** > > ** ** > > James**** > > ______________________________________________________________________ > PLEASE READ: This email is confidential and may be privileged. It is > intended for the named addressee(s) only and access to it by anyone else is > unauthorised. If you are not an addressee, any disclosure or copying of the > contents of this email or any action taken (or not taken) in reliance on it > is unauthorised and may be unlawful. If you have received this email in > error, please notify the sender or [email protected]. Email is not > a secure method of communication and the Company cannot accept > responsibility for the accuracy or completeness of this message or any > attachment(s). Please check this email for virus infection for which the > Company accepts no responsibility. If verification of this email is sought > then please request a hard copy. Unless otherwise stated, any views or > opinions presented are solely those of the author and do not represent > those of the Company. > > The Vernalis Group of Companies > 100 Berkshire Place > Wharfedale Road > Winnersh, Berkshire > RG41 5RD, England > Tel: +44 (0)118 938 0000 > > To access trading company registration and address details, please go to > the Vernalis website at www.vernalis.com and click on the "Company > address and registration details" link at the bottom of the page.. > ______________________________________________________________________ >
