I think it's in ShelxReader.java. Who will volunteer to look into this? Egon?
What is needed here is the sort of parsing that the CIF reader or PDB reader uses to get
atom.elementSymbol
probably using Atom.isValidElementSymbolNoCaseSecondCharacter()
But Pat is right that there is also another issue. The Li-O distances here are about 1.9 A. This compares well with others I know (listed in pm):
http://www.stolaf.edu/depts/chemistry/mo/struc/explore.htm?bond=Li-O
In this data set, the Li-O bond ranges in length between 188.3 and 249.4 pm.
Li-O 188 tetrahedral (C4H8O)4Li+ tetrakis(tetrahydrofuran)lithium cation Li-O 196 square pyramidal (C18H32O4)Li(NCS) Li-O 213 square pyramidal (C8H16O4)LiCl (12- crown- 4)- chloro- lithium Li-O 222 square antiprism (C8H16O4)2Li+ bis(12- crown- 4)- lithium cation
Since the O covalent radius is set at 68 pm, for these to show, with the 45 pm tolerance, we would need a radius of... 113 + about 110 pm for Li. I suggest the lithium covalent radius get changed to what Pat suggests, 120 pm, i.e. 1200 mar, with a comment added that it was for these purposes.
Bob Hanson
Pat Carroll wrote:
Bob,
I've attached a PDB file and a RES file for that Eu compound - the PDB file will have all the bonds drawn in explicitly. Jmol also has trouble with the Li atom in this molecule, but that's understandable - the covalent radius for Li in Javaconstants.java (0.68 A) is too small, it should be something like 1.2.
BTW, Jmol10pre8 draws the bonds to Eu correctly!!
Thanks, Pat
--
Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr
"Imagination is more important than knowledge." - Albert Einstein
------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
