Hi Ian,
You are right, here I was too quick. The orthogonal, not the submitted
coordinates are present in the PDB file. This means that one would indeed need
to transform the SCALE records and either delete or transform the SMTRY records
as well. Leaves the question why one would like to store the ORIGX records if
only the depositor and the PDB annotators ever see the submitted coordinates.
Best,
Herman
________________________________
From: Ian Tickle [mailto:[email protected]]
Sent: Wednesday, March 13, 2013 4:07 PM
To: Schreuder, Herman R&D/DE
Cc: [email protected]
Subject: Re: [ccp4bb] Best practice for transformed PDB coordinates?
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, <[email protected]> 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:[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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