> Nor I. I suggested in a previous e-mail that the Jmol Display/Spacefill/ > menu include several options: AnisoTemp, Covalent, vdWaals, and Ionic
'spacefill on' uses vanderwaals 'spacefill ionic' was going to be a combination of ionic and covalent I wondered whether the name should be changed to something else, since it was/is a combination of ionic and covalent. From my (very naive) perspective, that made sense ... since I have come to the (perhaps erroneous) conclusion that a covalent radius is just an ionic radius with charge 0. If this doesn't make sense, then we (the group) will rewind the discussion and go through it step-by-step until we (the group) are in general agreement. >> 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. > > Jmol is opening up the opportunity to use ionic radii for bonding > calculations whenever atom charge is explicitly specified in the data > file, but defaults to covalent radius for bonding in other circumstances > for backward compatibility with Chime/RasMol. (I doubt that 0.11 A > should change much, but I think that Miguel intends that Jmol thereby > maintains compatibility w/ OpenBabel--haven't doublechecked the code.) Correct. There are two cases where Jmol applies its 'autobond' algorithm 1. no bond information is specified in the file independent of the file type .xyz files never have bond connectivity 2. in the special case of .pdb files, when there are an 'insufficient' number of CONECT records (I am *not* using the same decision criteria as RasMol/Chime ... that is a separate discussion we can have if/when we need to) So, if there is atomic charge information in the file, what radii are used and what is the algorithm? I would like to use the same algorithm that I am currently using, hence my implementation of: distance >= 0.4 angstroms AND distance <= bondingRadius1 + bondingRadius2 + 0.45 angstroms where bondingRadiusN = if (charged and ionic entry exists) then ionic radius entry else covalent radius entry > Chime and RasMol make a mess of aluminosilicates (essentially oxides of > silicon and aluminum...the subject matter that Linus Pauling addressed > in the 20s and 30s when he was working on the nature of the chemical > bond (!). The values of covalent radii for silicon and aluminum are so > big that they force Si-Si, Al-Al, and Si-Al bonds in the oxides--nasty. > By using standard values of ionic radii (Pauling radii, they're > sometimes called), this shouldn't happen. What does Jmol do with these? > Thanks, I'd wondered what the fast and complex algorithms of RasMol and > Chime were! Certainly the fact that the 'fast' algorithm is applied when there are >256 atoms does not make any sense these days. 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
