Patrick wrote: > I've noticed that Jmol draws space-filling models with what look like > rather larger van der Waal's radii than you would expect. If you look > at: > > http://macxray.chem.upenn.edu/tutorial/basepair.html > > and change all the atoms to 100% VDW, the H's are really totally buried > in the atoms to which they are hydrogen bonded.
The vdwRadius values that we are using are taken from OpenBabel. Recently, there was some discussion on the OpenBabel list because someone thought that some of the numbers were off. > If I use the same PDB > file in rasmol, I get a more reasonable looking display. I don't know what the RasMol numbers are. I know that some of the RasMol radii are larger than they should be ... because Roger is trying to make up for the fact that .PDB files do not have hydrogen atoms. NOTE! It would be great if someone would volunteer to look up the VDW and covalent bonding radii in an accepted reference text. For the ionic radii we are using: * This data is from * Handbook of Chemistry and Physics. 48th Ed, 1967-8, p. F143 * (scanned for Jmol by Phillip Barak, Jan 2004) ****************************************************************/ I can easily send the current values to someone ... > The VDW radii > displayed in the "Atom Properties" item on the "edit" menu in the Jmol > application up to version 9 are reasonable, but the display looks > "wrong". I seriously doubt if those values are even being used in Jmol 9. > BTW, that menu item is "gone" from Jmol 10? (it would be nice > to be able to adjust Atom Properties). Jmol will probably be able to support this kind of thing in the 'not near' future ... through loading the values from a text file. Then, someone can put a nice table display on top of it. Miguel ------------------------------------------------------- This SF.Net email is sponsored by: IBM Linux Tutorials Free Linux tutorial presented by Daniel Robbins, President and CEO of GenToo technologies. Learn everything from fundamentals to system administration.http://ads.osdn.com/?ad_id=1470&alloc_id=3638&op=click _______________________________________________ Jmol-users mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-users
