> SHELXL .res files do not have any charge info (as several respondents have
> remarked). Generally, to draw bonds to metals, the covalent radius is used
> and usually there is a rather large tolerance to what is considered
> bonding
> distance (maybe 20-25% of the sum of the covalent radii). For the most
> part, this enables the correct drawing of the great majority of bonds (and
> this also takes into account differences in covalent radii due to charge).
OK
> But it appears that Jmol does not use the covalent radii to decide bonding
> distances - the covalent radii stored in Jmolconstants.java are reasonable
> (a no. of them are even overestimated).
Jmol does use the covalent radii to determine bonding when no charge data
is present.
It uses the ionic bonding radii when charge data is present.
For each atom it gets the bondingRadius (based upon the rules above)
if ((distance < (bondingRadiusA + bondingRadiusB + 0.45) &&
(distance > 0.4))
form a bond
> For example, I have a Europium
> compound with Eu-O bond distances of 2.2 - 2.3 Angstroms; the covalent
> radii for Eu and O in Jmolconstants are 1.99 + 0.68 = 2.67 ! There must be
> something else going on!
Don't know.
Send me a small file offlist.
Miguel
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