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Dear James,

if I understand correctly you want to transform structure B onto
structure A and then compare the crystallographic packing of A and B.
I might be wrong, but I think the most convenient way for the users
would be a display program which can handle two different global
coordinate systems (that of A and that of B) so that the symmetry
operators of B recreate the original crystal packing of B _after_ it was
mapped onto A.

I am not aware of a program which handles such two different global
coordinate systems, and if I am correct your last assumption is correct:
you have to "[..] accept that my aligned coordinates should no longer
be expected to recreate the packing environment [...]"

If you want to keep track within the PDB-file, maybe for later
reference, you could just add REMARK cards that explain what you did,
i.e. contain the original PDB-ID, transformation operator and the
reference PDB-ID.

As a work-around in case I did understand you correctly, you could
save the contacting symmetry equivalents of B into its own PDB file
(e.g. in coot) _before_ the transformation, then apply the
transformation so that the contacting molecules are transformed the
same way as B.

If somebody has a shorter way, I am happy to learn.

Best regards,
Tim

On 03/13/2013 01:57 PM, James Davidson 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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Institut fuer anorganische Chemie
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