Ah: Also added in there is a bondTolerance of 0.45 Angstroms.
In modelmanager.java we have:
public float bondTolerance = 0.45f;
and in datamodel/frame.java:
float maxAcceptable = bondingRadiusA + bondingRadiusB + bondTolerance;
So
2.67+0.45 = 3.12
right on the cutoff I was seeing. I think it's working properly.
Bob
Bob Hanson wrote:
Pat,
Well, that is curious. My test shows up a Eu-O bond at anything less than about 3.1 Angstroms. So actually, Jmol is being pretty generous there as well. I don't think it's possible that you could have a Eu-O bond that is not showing up if it is only 2.3 Angstroms apart. Something else must be going on with this file. Mine was an XYZ file, but that shouldn't have anything to do with it.
Could you forward that .res file to me so I can take a look at it? (off-list, please).
Bob Hanson
Patrick J. Carroll wrote:
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).
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). 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!
Pat Carroll
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