I have added the table of ionic radii to Jmol. - the table is what Phillip sent me: Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143
I trust you are keeping such literature references and sources in comments in the source code, and also in nascent documentation, Miguel.
The algorithm is as follows:
- if an atom has no charge, then the covalent radius is used
(data values from OpenBabel)
- if an atom has a charge, then it is looked up in the ionic table
* if it is not found in the ionic table, then the
covalent radius is returned
I may have missed (or forgotten) some of this discussion.
Are you talking about "used" for determining the presence of a covalent bond, or "used" in the spacefill rendering?
If the latter, do you really mean covalent radii?
As stated in
http://www.umass.edu/microbio/rasmol/rasbonds.htm
RasMol uses van der Waals radii or "united atom radii" by default for spacefill.
I think Jmol should do the same for backward compatibility.
I've never been clear about the rationale for using vdW radii in spacefill rendering instead of covalent radii.
I now need the following:
- small/simple files with charged atoms in the following formats
* xyz
* mol
* pdb
Not something I can easily provide. Phil?
Also, Miguel, I trust you are keeping a list of atomic coordinate files, and the files themselves, used for testing -- along with notes about what each illustrates. This will probably be very useful over and over.
- confirmation that the existing bonding algorithm will give
acceptable results:
bondingRadius1 + bondingRadius2 + 0.45 angstroms (tolerance)
Is "bondingRadiusN" a covalent radius? This is what RasMol/Chime use (http://www.umass.edu/microbio/rasmol/rasbonds.htm). But where did you get 0.45 A? R/C use 0.56 A according to the above doc.
In fact, as also documented in rasbonds.htm, for all macromolecules, covalent
bonds are drawn for any two atoms between 0.4-1.9 Angstroms apart. I'd be somewhat nervous about changing this default only because I have no experience with the more sophisticated method -- the simpler method works most of the time quite well in my experience. My recollection is that the only reason Roger used the simpler method because he was worried about performance issues with the computers of the early 1990's. Probably not an issue now.
-Eric
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - Protein Explorer - 3D Visualization: http://proteinexplorer.org Workshops: http://www.umass.edu/molvis/workshop World Index of Molecular Visualization Resources: http://molvisindex.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://molvis.sdsc.edu/atlas/atlas.htm PDB Lite Macromolecule Finder: http://pdblite.org Molecular Visualization EMail List: http://www.umass.edu/microbio/rasmol/raslist.htm
Eric Martz, Professor Emeritus, Dept Microbiology
U Mass, Amherst MA US 413-545-2325/FAX 413-545-2532
http://www.umass.edu/molvis/martz
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