In the early days of the PDB coordinates were submitted
in many different coordinate systems:
orthogonal
fractional
grid (normalize each cell edge to 100 so that all coordinates
are between 0 and 100)
build physical model using 2 cm per Angstrom parts and then
measure coordinates using a ruler that measures inches
[I'm not kidding - I processed that one]
orthogonal but author wanted a rotation
etc.
After processing the first 100 or so entries in a format
based on the output of Diamond real-space refinement, we
realized that a better format was needed. In designing what
is now known as "PDB format" we decided that crystallographers
could cope with coordinates in any frame but everyone else needed
to have the coordinates in orthognal Angstroms so that they could
compute distances, etc. without a lot of headscratching. So we
decided to have all entries store coordinates in an orthognal
Angstrom frame.
ORIGX is the transformation that takes the coordinates in
the entry back to the coordinates that were submitted. I would
guess that almost all entries now have an identity transformation
for ORIGX but the earliest entries have all sorts of transformations
in ORIGX. [Another way of viewing ORIGX is that it is the inverse
of the transformation that generated the entry from the deposition.]
SCALE is the transformation that generates fractional coordinates
from the orthogonal Angstrom coordinates in the entry. I am sure
that SCAlE is the default that one could generate from CRYST1 in
most cases but definitely not in all cases.
Hope that helps.
Frances
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