Hi Herman Yes your solution would also work, and is also safer in the event that other programs don't know how to handle SCALE & ORIGX records correctly: you are just using ORIGX to store the transformation & leave the co-ordinates alone.
I was imagining that James might want to do further work with the transformed co-ordinates, so I guess the answer is that it all depends on what you plan to do with the file. As I said, my solution makes the assumption (possibly rash!) that the graphics & other programs treat the SCALE & ORIGX records correctly. Actually in my scheme it's only the SCALE records that matter (since these are actually what transforms orth -> fract for the symmetry to operate on): the ORIGX records are only needed as a reference back to the original co-ordinates and can be safely ignored. Cheers -- Ian On 13 March 2013 14:51, <herman.schreu...@sanofi.com> wrote: > ** > Dear Ian, > > As I see it, there is no need to change the orthogonal coordinates. They > are used in connection with the SYMTRY records to generate the symmetry > mates. Changing the orthogonal coordinates would mean changing the SYMTRY > records, which would only complicate things. If we do not change the > orthogonal coordinates, we do not need to change the SCALE matrix and the > only thing we need to change is the ORIGX matrix. > > Since the ORIGX matrix is defined as the matrix transforming the > orthogonal to submitted coordinates, this is exactly the superposition > matrix used to transform the original orthogonal coordinates to get these > submitted coordinates. > > Please correct me if I am wrong! > Herman > > ------------------------------ > *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Ian > Tickle > *Sent:* Wednesday, March 13, 2013 3:33 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Best practice for transformed PDB coordinates? > > 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 <j.david...@vernalis.com> 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. 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