slow day, time for a flame war

["David J. Schuller" <schuller@uci.edu>]

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On Fri, 25 Jun 1999, Brent Segelke wrote:

> ...   I wonder how many people just aren't committed enough
> to the idea of NCS.  People want to give up on NCS very quickly, or at least
> loosen their restraints, saying that there is some real difference between
> NCS copies of their molecule.  I think what their seeing is that it's more
> difficult to get the Rvalue down to the desired value with strong NCS.

i don't which 'people' you are talking about, but i hope you will agree
that you are over-generalizing.  I am committed to the idea of NCS _AND_
I am finishing up my second structure with large and significant deviation
from the NCS in regions of the molecule.  for example check out 1SCH.
sorry, i just couldn't get that 12 degree rotation of the active site
cleft between 2 domains to go away.  this eventually led to the ability of
magicsquash and then dm to handle multiple domain NCS.

it would be easier if the software were more in tune with people's needs.
for example, i think refinement with strict constraints ought to account
for refinement of the NCS matrix. the way this is handled in X-plor for
instance is extremely cumbersome.  to do rigid body refinement one needs
coordinates for each molecule, and has to go through the whole "generate"
BS. (am i the only one who has wondered why it is necessary in X-plor to
generate complete model geometry just to calculate a map?)
 Then, to do minimization or simulated annealing with strict
constraints, one has to switch to coordinates of a single molecule, with
the symmetry mates generate by the constraints, so
that it is necessary to repeat the "generate" step again.  this makes it
laborious to toss in a few rounds of rigid body in between regular
refinement.

NCS restraints are much easier to use for the above reason, and also
because they can be applied only to certain portions of the molecule if
necessary.  maybe the reason people give up on constraints so easily is
that they have severe limitations in real world use.

cheers,

=======================================================================
"Being able to put two rounds into the same hole from 25 meters! That's
gun control." - Jesse Ventura, before becoming governor of Minnesota
=======================================================================
                        David J. Schuller
                        modern man in a post-modern world
                        University of California-Irvine
                        schuller@uci.edu