Dear Ian,
My feeling is that most crystallograpic programs use indeed a separate
library with symmetry operators acting on fractional coordinates.
However, the SMTRY records in the PDB files work on the orthogonal
coordinates and some of the more advanced non-crystallographic
viewing/modeling programs use these to generate symmetry mates. In this
way, those non-crystallographic programs do not need to provide
libraries with symmetry operators and they do not need to bother whether
one has a hexagonal or rombohedral settings or whether the space group
is P21212 or P22121. If crystallographers would be using these records
as well, there would have been a lot less confusion, but that is another
story.
So to be on the safe side, one would need to either delete or transform
the SMTRY records.
Cheers,
Herman
________________________________
From: Ian Tickle [mailto:ianj...@gmail.com]
Sent: Wednesday, March 13, 2013 4:22 PM
To: Schreuder, Herman R&D/DE
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Best practice for transformed PDB
coordinates?
On 13 March 2013 14:51, <herman.schreu...@sanofi.com> wrote:
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.
PS note there is no need to change the symmetry operators in
either scheme, because these actually operate on the fractional
co-ordinates, not directly on the orthogonal ones. In my scheme I
redefine the SCALE matrix so that together with the transformed
co-ordinates you recover the original fractional co-ordinates and so the
symmetry still works correctly (theoretically of course!).
Cheers
-- Ian
