> 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.
Well, not really. The fact is, I won't recognize errors unless they are pretty obvious. One difference I did spot was in hemoglobin heme. Jmol binds the iron atom and RasMol/Chime does not. I asked someone and was told that the Jmol behavior was correct. >> - confirmation that the existing bonding algorithm will give >> acceptable results: >> bondingRadius1 + bondingRadius2 + 0.45 angstroms (tolerance) > > Is "bondingRadiusN" a covalent radius? bondingRadiusN is: - If the atom has a a charge *and* the element/charge combination exists in the the ionic radius table, then use that value - otherwise, use the 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. I have never seen this document. 0.45 A was taken from OpenBabel. I had some mailing-list exchange with them regarding this. I have subsequently seen literature references from 0.4 to 0.5. 0.56 is larger than anything else I have seen. > 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. Hmmm ... that doesn't seem right to me. It certainly won't work for files that have hydrogens. The distances between the hydrogens on a tetrahedral carbon are less than 1.9 Angstroms. > 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. To date there have not been complaints from Jmol users (although admittedly there have not been a large number of Jmol users). I will take a look at the RasMol source and see exactly what is going on. Recall that the RasMol algorithm does not correctly recognize S-S bonds, whereas Jmol does. > 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. That is what Roger said to me when I asked about the S-S bond issue. Frankly, I didn't understand why applying element-specific covalent bonding radii would have been a performance issue ... I'll take a look at the RasMol source. Miguel ------------------------------------------------------- This SF.net email is sponsored by: Perforce Software. Perforce is the Fast Software Configuration Management System offering advanced branching capabilities and atomic changes on 50+ platforms. Free Eval! http://www.perforce.com/perforce/loadprog.html _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
