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.
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