Pat, VDW radii are used for many things, not just spacefill. So I'm reticent to do any global change to any of these numbers. But, yes, that's an issue. Let's discuss it again.
The Jmol code comments state that the values used are from OpenBabel. However, when I look at openbabel-2.1.1/data/element.txt, that's not what I see. So I don't know what that is about. First, Jmol is not using the VDW radii from OpenBabel. Second, some are larger, some smaller; they aren't "generally larger" or "generally smaller". I've also compared Jmol's values to openRasmol. Here's the comparison of these three packages: http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/src/org/jmol/_documents/vdw_comparison.xls Options include: a) include one or more optional sets of VDW radii b) include the option for the user to set individual VDW radii c) leave as is -- just defining the spacefill as you suggest, one element at a time Bob Patrick J. Carroll wrote: >I remember a discussion a couple years ago about the van der Waal's radii used >in Jmol. There was a feeling that the values in Jmol are somewhat >"over-estimated". Is there a way that a user can input his own radii? (other >than using the explcit "spacefill 1.70" every time he wants to draw a van der >Waals carbon atom). Or, alternatively, can the values in JmolConstants.jave be >changed to those in, e.g., A. Bondi, J. Phys. Chem, vol.68, p.441 (1964) - >which, I think, are widely accepted. > > >Pat Carroll >U of Penn >Phila, PA > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
