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Re: [ccp4bb]: NCS analysis

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On Thu, 3 Feb 2000, M.D.Winn wrote:

> Reply to Trixie Wagner bw6f@unix.mail.virginia.edu
> > 
> > I am working on the structure of a tetramer with non-crystallographic 222
> > symmetry. It is not difficult to determine the three two-fold axes
> > separately by superimposing dimers, but 
> > a) they are not necessarily perpendicular to each other and/or might not
> >    intersect in one point and 
> > b) from the direction cosines of the axes you cannot conclude where
> >    exactly to put the two-folds with respect to the tetramer (i.e. 
> >    where the origin of the 222 system is located).
> > 
> > I would need this information e.g. to compare two of my structures by
> > superimposing their 222 axes.
> > 
> > So, basically, my question is, does anybody know about a program which
> > extracts the best 222 axes set from my coordinates?

if you have 222 symmetry, then i believe your axes ARE necessarily
perpendicular.  isn't that how it is defined?

how do you know about the 222 symmetry?  from the self-rotation
function?  you must remember that it does not include the translational

1) perhaps you do have a 222 tetramer, but have not yet selected the
copies of A,B,C,D that go together.

2) another possibility is that you do actually have a 222 tetramer, but
that it includes elements of both the crystallographic (about which you
have told us nothing) and noncrystallographic symmetry. in this case the 4
monomers in the asymmetric unit would not be part of the same tetramer.
(e.g. tetramers might be ABAB and CDCD)

3) are you quite sure that the relevant form of your protein is a
tetramer?  is it possible instead that it is a dimer, and what you are
seeing in the crystal is a 'dimer if dimers'?  if this might be the case,
you could investigate it by comparing the contact surface area between
various pairs of monomers, for instance. using the term 'axis'
instead of 'transformation' in regards to NCS symmetry preconditions one
to think in terms of proper symmetry.  beware of this trap.

in any of these cases, i would suggest looking at a large chunk of volume,
with symmetry-related molecules displayed, preferably with a program that
lets you color-code the monomers.  perhaps throw in some pseudo-atoms or
lines to denote the 2-fold axes, if your software allows.  this is going 
to be huge, so if possible display only Ca traces or backbones instead of
the full molecules.
look for compactness. 

"interventionism is the spawning pool of international terror" - Pat Buchanan
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine