Relativistic velocities

Aaron Oakley s_aarono at EDUSERV.ITS.UNIMELB.EDU.AU
Tue Apr 1 21:28:43 EST 1997


> 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

I understand that bond lengths can deviate systematically from the
mean if there is an error in the cell used in the refinement.
In your case the unit cell might be a little bit too small.

> 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? 

It seems to me that something is seriously wrong. I don't think
that X-PLOR takes relativistic effects into account.
An R-free of 72 % seems way too high. Do you only have data
to 4 Ang. resolution? You may not have enough data to perform
simulated annealing.

Cheers,

Aaron




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