Dear James,
I checked the PDB documentation. Putting the transformation in the ORIGX1,2,3
records should do the trick. However, I wonder if there is any program around
which actually reads and applies the ORIGX1,2,3 transformation. Maybe the
coot/pymol/ccp4mg people could comment? My safest bet would be to generate the
symmetry molecule in its original setting and then transform both original
molecule and symmetry mate using the superposition matrix.
On the other hand, it is not much work to put the transformation matrix in the
ORIGX1,2,3 records and see what happens. One could open two coot windows: one
with the original coordinates and one with the transformed coordinates and
check that in both cases the same symmetry mates are being generated.
Herman
________________________________
From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of
James Davidson
Sent: Wednesday, March 13, 2013 1:58 PM
To: [email protected]
Subject: [ccp4bb] Best practice for transformed PDB coordinates?
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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