Hello Xiang I have no experience with Alchemy format, but yes it looks like a problem with the file reader. And I agree with Rolf, you have overlapping atoms, and "select all" reports 13 atoms. You should clean up your alc file.
You have several ways to do this in Jmol (apart from having the file reader work): a) define your "bonds" in JmolScript, which can be provided in a script or maybe embedded in the molecular file connect (atomno=1) (atomno=2,atomno=4,atomno=5) etc. b) draw lines instead of bonds draw (atomno=1) (atomno=2) (atomno=3) (atomno=4) noFill mesh etc. c) in this example, it is enough to have Jmol draw the boundbox (will not work in other files less symmetrical): boundbox on boundbox 0.03; color boundbox orange To prevent Jmol from drawing any bonds before you define your own, use connect (*) (*) delete Reference: a) http://www.stolaf.edu/academics/chemapps/jmol/docs/#connect b) http://www.stolaf.edu/academics/chemapps/jmol/docs/#draw c) http://www.stolaf.edu/academics/chemapps/jmol/docs/#boundbox Hope it is of help. In any case, you should check your file against some correct molecule file in Alchemy and see if there is a bug in Jmol reader, then report it. ------------------------------------------------------------------------------ SF.Net email is Sponsored by MIX09, March 18-20, 2009 in Las Vegas, Nevada. The future of the web can't happen without you. Join us at MIX09 to help pave the way to the Next Web now. Learn more and register at http://ad.doubleclick.net/clk;208669438;13503038;i?http://2009.visitmix.com/ _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users