Calculate the variance of all pairwise distances in an ensemble of
Cartesian coordinates.

var.xyz(xyz, weights=TRUE)
var.pdbs(pdbs, ...)

## Arguments

xyz |
an object of class `"xyz"` containing Cartesian
coordinates in a matrix. |

weights |
logical, if TRUE weights are calculated based on the
pairwise distance variance. |

pdbs |
a ‘pdbs’ object as object from function
`pdbaln` . |

... |
arguments passed to associated functions. |

## Details

This function calculates the variance of all pairwise distances in an
ensemble of Cartesian coordinates. The primary use of this function is
to calculate weights to scale the pair force constant for NMA.

## Value

Returns the a matrix of the pairwise distance variance, formated as
weights if ‘weights=TRUE’.

## References

Grant, B.J. et al. (2006) *Bioinformatics* **22**, 2695--2696.

## Author

Lars Skjaerven

## See also