machius at CHOP.SWMED.EDU
Tue Apr 1 19:44:57 EST 1997
Hi X-PLORers !
After refinement of a protein structure, we observed that all bond lengths
were a little bit too short, i.e. we did not see a normal distribution
around the equilibrium lengths. Our first refinement step was a simulated
annealing at 4 Ang where we realized that the free R-factor went up to 72%
at a temperature around 4000 K with atom velocities of about 2.5*10^6
Ang/ps. We had to modify X-PLOR partially in order to get this number
printed in our output files. The question is whether the final short bond
lengths are due to the "relativistic length contraction" at these high
velocities. Furthermore, under relativistic conditions, the mass of atoms
is supposed to be increased. How does X-PLOR handle this aspect and the
corresponding changes in the force constants?
We also had a rather large mean error in the coordinates. Is this due to
the fact that at high velocities the positions of the atoms cannot be
determined accurately because of Heisenberg's uncertainty principle?
Any delighting comments are very welcome.
Happy X-PLORing !
More information about the X-plor