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:[email protected]] On Behalf Of
Ian Tickle
Sent: Wednesday, March 13, 2013 3:33 PM
To: [email protected]
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 <[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
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