From: Adrian Koh (kohsj_at_ihpc.a-star.edu.sg)
Date: Wed Feb 16 2005 - 02:29:09 CST

Dear all,

I have with me the xyz-coordinates of a list of atoms in the .xyz
format. I'd like to add bonds between some atoms, how can this be
done? I've attached a sample file for your reference.

Thanks!

Adrian.

441
        Generated by KSJ
        Pt -7.84 0 0 7.84 Radius = 7.84
        Pt -5.88 -1.96 0 6.198064214
        Pt -5.88 1.96 0 6.198064214
        Pt -3.92 -3.92 0 5.543717165
        Pt -3.92 0 0 3.92
        Pt -3.92 3.92 0 5.543717165
        Pt -1.96 -5.88 0 6.198064214
        Pt -1.96 -1.96 0 2.771858582
        Pt -1.96 1.96 0 2.771858582
        Pt -1.96 5.88 0 6.198064214
        Pt 0 -7.84 0 7.84
        Pt 0 -3.92 0 3.92
        Pt 0 0 0 0
        Pt 0 3.92 0 3.92
        Pt 0 7.84 0 7.84
        Pt 1.96 -5.88 0 6.198064214
        Pt 1.96 -1.96 0 2.771858582
        Pt 1.96 1.96 0 2.771858582
        Pt 1.96 5.88 0 6.198064214
        Pt 3.92 -3.92 0 5.543717165
        Pt 3.92 0 0 3.92
        Pt 3.92 3.92 0 5.543717165
        Pt 5.88 -1.96 0 6.198064214
        Pt 5.88 1.96 0 6.198064214
        Pt 7.84 0 0 7.84
        Pt -5.88 -3.92 1.96 7.0668805
        Pt -5.88 0 1.96 5.88
        Pt -5.88 3.92 1.96 7.0668805
        Pt -3.92 -5.88 1.96 7.0668805
        Pt -3.92 -1.96 1.96 4.382693236
        Pt -3.92 1.96 1.96 4.382693236
        Pt -3.92 5.88 1.96 7.0668805
        Pt -1.96 -3.92 1.96 4.382693236
        Pt -1.96 0 1.96 1.96
        Pt -1.96 3.92 1.96 4.382693236
        Pt 0 -5.88 1.96 5.88
        Pt 0 -1.96 1.96 1.96
        Pt 0 1.96 1.96 1.96
        Pt 0 5.88 1.96 5.88
        Pt 1.96 -3.92 1.96 4.382693236
        Pt 1.96 0 1.96 1.96
        Pt 1.96 3.92 1.96 4.382693236
        Pt 3.92 -5.88 1.96 7.0668805
        Pt 3.92 -1.96 1.96 4.382693236
        Pt 3.92 1.96 1.96 4.382693236
        Pt 3.92 5.88 1.96 7.0668805
        Pt 5.88 -3.92 1.96 7.0668805
        Pt 5.88 0 1.96 5.88
        Pt 5.88 3.92 1.96 7.0668805
        Pt -7.84 0 3.92 7.84
        Pt -5.88 -1.96 3.92 6.198064214
        Pt -5.88 1.96 3.92 6.198064214
        Pt -3.92 -3.92 3.92 5.543717165
        Pt -3.92 0 3.92 3.92
        Pt -3.92 3.92 3.92 5.543717165
        Pt -1.96 -5.88 3.92 6.198064214
        Pt -1.96 -1.96 3.92 2.771858582
        Pt -1.96 1.96 3.92 2.771858582
        Pt -1.96 5.88 3.92 6.198064214
        Pt 0 -7.84 3.92 7.84
        Pt 0 -3.92 3.92 3.92
        Pt 0 0 3.92 0
        Pt 0 3.92 3.92 3.92
        Pt 0 7.84 3.92 7.84
        Pt 1.96 -5.88 3.92 6.198064214
        Pt 1.96 -1.96 3.92 2.771858582
        Pt 1.96 1.96 3.92 2.771858582
        Pt 1.96 5.88 3.92 6.198064214
        Pt 3.92 -3.92 3.92 5.543717165
        Pt 3.92 0 3.92 3.92
        Pt 3.92 3.92 3.92 5.543717165
        Pt 5.88 -1.96 3.92 6.198064214
        Pt 5.88 1.96 3.92 6.198064214
        Pt 7.84 0 3.92 7.84
        Pt -5.88 -3.92 5.88 7.0668805
        Pt -5.88 0 5.88 5.88
        Pt -5.88 3.92 5.88 7.0668805
        Pt -3.92 -5.88 5.88 7.0668805
        Pt -3.92 -1.96 5.88 4.382693236
        Pt -3.92 1.96 5.88 4.382693236
        Pt -3.92 5.88 5.88 7.0668805
        Pt -1.96 -3.92 5.88 4.382693236
        Pt -1.96 0 5.88 1.96
        Pt -1.96 3.92 5.88 4.382693236
        Pt 0 -5.88 5.88 5.88
        Pt 0 -1.96 5.88 1.96
        Pt 0 1.96 5.88 1.96
        Pt 0 5.88 5.88 5.88
        Pt 1.96 -3.92 5.88 4.382693236
        Pt 1.96 0 5.88 1.96
        Pt 1.96 3.92 5.88 4.382693236
        Pt 3.92 -5.88 5.88 7.0668805
        Pt 3.92 -1.96 5.88 4.382693236
        Pt 3.92 1.96 5.88 4.382693236
        Pt 3.92 5.88 5.88 7.0668805
        Pt 5.88 -3.92 5.88 7.0668805
        Pt 5.88 0 5.88 5.88
        Pt 5.88 3.92 5.88 7.0668805
        Pt -7.84 0 7.84 7.84
        Pt -5.88 -1.96 7.84 6.198064214
        Pt -5.88 1.96 7.84 6.198064214
        Pt -3.92 -3.92 7.84 5.543717165
        Pt -3.92 0 7.84 3.92
        Pt -3.92 3.92 7.84 5.543717165
        Pt -1.96 -5.88 7.84 6.198064214
        Pt -1.96 -1.96 7.84 2.771858582
        Pt -1.96 1.96 7.84 2.771858582
        Pt -1.96 5.88 7.84 6.198064214
        Pt 0 -7.84 7.84 7.84
        Pt 0 -3.92 7.84 3.92
        Pt 0 0 7.84 0
        Pt 0 3.92 7.84 3.92
        Pt 0 7.84 7.84 7.84
        Pt 1.96 -5.88 7.84 6.198064214
        Pt 1.96 -1.96 7.84 2.771858582
        Pt 1.96 1.96 7.84 2.771858582
        Pt 1.96 5.88 7.84 6.198064214
        Pt 3.92 -3.92 7.84 5.543717165
        Pt 3.92 0 7.84 3.92
        Pt 3.92 3.92 7.84 5.543717165
        Pt 5.88 -1.96 7.84 6.198064214
        Pt 5.88 1.96 7.84 6.198064214
        Pt 7.84 0 7.84 7.84
        Pt -5.88 -3.92 9.8 7.0668805
        Pt -5.88 0 9.8 5.88
        Pt -5.88 3.92 9.8 7.0668805
        Pt -3.92 -5.88 9.8 7.0668805
        Pt -3.92 -1.96 9.8 4.382693236
        Pt -3.92 1.96 9.8 4.382693236
        Pt -3.92 5.88 9.8 7.0668805
        Pt -1.96 -3.92 9.8 4.382693236
        Pt -1.96 0 9.8 1.96
        Pt -1.96 3.92 9.8 4.382693236
        Pt 0 -5.88 9.8 5.88
        Pt 0 -1.96 9.8 1.96
        Pt 0 1.96 9.8 1.96
        Pt 0 5.88 9.8 5.88
        Pt 1.96 -3.92 9.8 4.382693236
        Pt 1.96 0 9.8 1.96
        Pt 1.96 3.92 9.8 4.382693236
        Pt 3.92 -5.88 9.8 7.0668805
        Pt 3.92 -1.96 9.8 4.382693236
        Pt 3.92 1.96 9.8 4.382693236
        Pt 3.92 5.88 9.8 7.0668805
        Pt 5.88 -3.92 9.8 7.0668805
        Pt 5.88 0 9.8 5.88
        Pt 5.88 3.92 9.8 7.0668805
        Pt -7.84 0 11.76 7.84
        Pt -5.88 -1.96 11.76 6.198064214
        Pt -5.88 1.96 11.76 6.198064214
        Pt -3.92 -3.92 11.76 5.543717165
        Pt -3.92 0 11.76 3.92
        Pt -3.92 3.92 11.76 5.543717165
        Pt -1.96 -5.88 11.76 6.198064214
        Pt -1.96 -1.96 11.76 2.771858582
        Pt -1.96 1.96 11.76 2.771858582
        Pt -1.96 5.88 11.76 6.198064214
        Pt 0 -7.84 11.76 7.84
        Pt 0 -3.92 11.76 3.92
        Pt 0 0 11.76 0
        Pt 0 3.92 11.76 3.92
        Pt 0 7.84 11.76 7.84
        Pt 1.96 -5.88 11.76 6.198064214
        Pt 1.96 -1.96 11.76 2.771858582
        Pt 1.96 1.96 11.76 2.771858582
        Pt 1.96 5.88 11.76 6.198064214
        Pt 3.92 -3.92 11.76 5.543717165
        Pt 3.92 0 11.76 3.92
        Pt 3.92 3.92 11.76 5.543717165
        Pt 5.88 -1.96 11.76 6.198064214
        Pt 5.88 1.96 11.76 6.198064214
        Pt 7.84 0 11.76 7.84
        Pt -5.88 -3.92 13.72 7.0668805
        Pt -5.88 0 13.72 5.88
        Pt -5.88 3.92 13.72 7.0668805
        Pt -3.92 -5.88 13.72 7.0668805
        Pt -3.92 -1.96 13.72 4.382693236
        Pt -3.92 1.96 13.72 4.382693236
        Pt -3.92 5.88 13.72 7.0668805
        Pt -1.96 -3.92 13.72 4.382693236
        Pt -1.96 0 13.72 1.96
        Pt -1.96 3.92 13.72 4.382693236
        Pt 0 -5.88 13.72 5.88
        Pt 0 -1.96 13.72 1.96
        Pt 0 1.96 13.72 1.96
        Pt 0 5.88 13.72 5.88
        Pt 1.96 -3.92 13.72 4.382693236
        Pt 1.96 0 13.72 1.96
        Pt 1.96 3.92 13.72 4.382693236
        Pt 3.92 -5.88 13.72 7.0668805
        Pt 3.92 -1.96 13.72 4.382693236
        Pt 3.92 1.96 13.72 4.382693236
        Pt 3.92 5.88 13.72 7.0668805
        Pt 5.88 -3.92 13.72 7.0668805
        Pt 5.88 0 13.72 5.88
        Pt 5.88 3.92 13.72 7.0668805
        Pt -7.84 0 15.68 7.84
        Pt -5.88 -1.96 15.68 6.198064214
        Pt -5.88 1.96 15.68 6.198064214
        Pt -3.92 -3.92 15.68 5.543717165
        Pt -3.92 0 15.68 3.92
        Pt -3.92 3.92 15.68 5.543717165
        Pt -1.96 -5.88 15.68 6.198064214
        Pt -1.96 -1.96 15.68 2.771858582
        Pt -1.96 1.96 15.68 2.771858582
        Pt -1.96 5.88 15.68 6.198064214
        Pt 0 -7.84 15.68 7.84
        Pt 0 -3.92 15.68 3.92
        Pt 0 0 15.68 0
        Pt 0 3.92 15.68 3.92
        Pt 0 7.84 15.68 7.84
        Pt 1.96 -5.88 15.68 6.198064214
        Pt 1.96 -1.96 15.68 2.771858582
        Pt 1.96 1.96 15.68 2.771858582
        Pt 1.96 5.88 15.68 6.198064214
        Pt 3.92 -3.92 15.68 5.543717165
        Pt 3.92 0 15.68 3.92
        Pt 3.92 3.92 15.68 5.543717165
        Pt 5.88 -1.96 15.68 6.198064214
        Pt 5.88 1.96 15.68 6.198064214
        Pt 7.84 0 15.68 7.84
        Pt -5.88 -3.92 17.64 7.0668805
        Pt -5.88 0 17.64 5.88
        Pt -5.88 3.92 17.64 7.0668805
        Pt -3.92 -5.88 17.64 7.0668805
        Pt -3.92 -1.96 17.64 4.382693236
        Pt -3.92 1.96 17.64 4.382693236
        Pt -3.92 5.88 17.64 7.0668805
        Pt -1.96 -3.92 17.64 4.382693236
        Pt -1.96 0 17.64 1.96
        Pt -1.96 3.92 17.64 4.382693236
        Pt 0 -5.88 17.64 5.88
        Pt 0 -1.96 17.64 1.96
        Pt 0 1.96 17.64 1.96
        Pt 0 5.88 17.64 5.88
        Pt 1.96 -3.92 17.64 4.382693236
        Pt 1.96 0 17.64 1.96
        Pt 1.96 3.92 17.64 4.382693236
        Pt 3.92 -5.88 17.64 7.0668805
        Pt 3.92 -1.96 17.64 4.382693236
        Pt 3.92 1.96 17.64 4.382693236
        Pt 3.92 5.88 17.64 7.0668805
        Pt 5.88 -3.92 17.64 7.0668805
        Pt 5.88 0 17.64 5.88
        Pt 5.88 3.92 17.64 7.0668805
        Pt -7.84 0 19.6 7.84
        Pt -5.88 -1.96 19.6 6.198064214
        Pt -5.88 1.96 19.6 6.198064214
        Pt -3.92 -3.92 19.6 5.543717165
        Pt -3.92 0 19.6 3.92
        Pt -3.92 3.92 19.6 5.543717165
        Pt -1.96 -5.88 19.6 6.198064214
        Pt -1.96 -1.96 19.6 2.771858582
        Pt -1.96 1.96 19.6 2.771858582
        Pt -1.96 5.88 19.6 6.198064214
        Pt 0 -7.84 19.6 7.84
        Pt 0 -3.92 19.6 3.92
        Pt 0 0 19.6 0
        Pt 0 3.92 19.6 3.92
        Pt 0 7.84 19.6 7.84
        Pt 1.96 -5.88 19.6 6.198064214
        Pt 1.96 -1.96 19.6 2.771858582
        Pt 1.96 1.96 19.6 2.771858582
        Pt 1.96 5.88 19.6 6.198064214
        Pt 3.92 -3.92 19.6 5.543717165
        Pt 3.92 0 19.6 3.92
        Pt 3.92 3.92 19.6 5.543717165
        Pt 5.88 -1.96 19.6 6.198064214
        Pt 5.88 1.96 19.6 6.198064214
        Pt 7.84 0 19.6 7.84
        Pt -5.88 -3.92 21.56 7.0668805
        Pt -5.88 0 21.56 5.88
        Pt -5.88 3.92 21.56 7.0668805
        Pt -3.92 -5.88 21.56 7.0668805
        Pt -3.92 -1.96 21.56 4.382693236
        Pt -3.92 1.96 21.56 4.382693236
        Pt -3.92 5.88 21.56 7.0668805
        Pt -1.96 -3.92 21.56 4.382693236
        Pt -1.96 0 21.56 1.96
        Pt -1.96 3.92 21.56 4.382693236
        Pt 0 -5.88 21.56 5.88
        Pt 0 -1.96 21.56 1.96
        Pt 0 1.96 21.56 1.96
        Pt 0 5.88 21.56 5.88
        Pt 1.96 -3.92 21.56 4.382693236
        Pt 1.96 0 21.56 1.96
        Pt 1.96 3.92 21.56 4.382693236
        Pt 3.92 -5.88 21.56 7.0668805
        Pt 3.92 -1.96 21.56 4.382693236
        Pt 3.92 1.96 21.56 4.382693236
        Pt 3.92 5.88 21.56 7.0668805
        Pt 5.88 -3.92 21.56 7.0668805
        Pt 5.88 0 21.56 5.88
        Pt 5.88 3.92 21.56 7.0668805
        Pt -7.84 0 23.52 7.84
        Pt -5.88 -1.96 23.52 6.198064214
        Pt -5.88 1.96 23.52 6.198064214
        Pt -3.92 -3.92 23.52 5.543717165
        Pt -3.92 0 23.52 3.92
        Pt -3.92 3.92 23.52 5.543717165
        Pt -1.96 -5.88 23.52 6.198064214
        Pt -1.96 -1.96 23.52 2.771858582
        Pt -1.96 1.96 23.52 2.771858582
        Pt -1.96 5.88 23.52 6.198064214
        Pt 0 -7.84 23.52 7.84
        Pt 0 -3.92 23.52 3.92
        Pt 0 0 23.52 0
        Pt 0 3.92 23.52 3.92
        Pt 0 7.84 23.52 7.84
        Pt 1.96 -5.88 23.52 6.198064214
        Pt 1.96 -1.96 23.52 2.771858582
        Pt 1.96 1.96 23.52 2.771858582
        Pt 1.96 5.88 23.52 6.198064214
        Pt 3.92 -3.92 23.52 5.543717165
        Pt 3.92 0 23.52 3.92
        Pt 3.92 3.92 23.52 5.543717165
        Pt 5.88 -1.96 23.52 6.198064214
        Pt 5.88 1.96 23.52 6.198064214
        Pt 7.84 0 23.52 7.84
        Pt -5.88 -3.92 25.48 7.0668805
        Pt -5.88 0 25.48 5.88
        Pt -5.88 3.92 25.48 7.0668805
        Pt -3.92 -5.88 25.48 7.0668805
        Pt -3.92 -1.96 25.48 4.382693236
        Pt -3.92 1.96 25.48 4.382693236
        Pt -3.92 5.88 25.48 7.0668805
        Pt -1.96 -3.92 25.48 4.382693236
        Pt -1.96 0 25.48 1.96
        Pt -1.96 3.92 25.48 4.382693236
        Pt 0 -5.88 25.48 5.88
        Pt 0 -1.96 25.48 1.96
        Pt 0 1.96 25.48 1.96
        Pt 0 5.88 25.48 5.88
        Pt 1.96 -3.92 25.48 4.382693236
        Pt 1.96 0 25.48 1.96
        Pt 1.96 3.92 25.48 4.382693236
        Pt 3.92 -5.88 25.48 7.0668805
        Pt 3.92 -1.96 25.48 4.382693236
        Pt 3.92 1.96 25.48 4.382693236
        Pt 3.92 5.88 25.48 7.0668805
        Pt 5.88 -3.92 25.48 7.0668805
        Pt 5.88 0 25.48 5.88
        Pt 5.88 3.92 25.48 7.0668805
        Pt -7.84 0 27.44 7.84
        Pt -5.88 -1.96 27.44 6.198064214
        Pt -5.88 1.96 27.44 6.198064214
        Pt -3.92 -3.92 27.44 5.543717165
        Pt -3.92 0 27.44 3.92
        Pt -3.92 3.92 27.44 5.543717165
        Pt -1.96 -5.88 27.44 6.198064214
        Pt -1.96 -1.96 27.44 2.771858582
        Pt -1.96 1.96 27.44 2.771858582
        Pt -1.96 5.88 27.44 6.198064214
        Pt 0 -7.84 27.44 7.84
        Pt 0 -3.92 27.44 3.92
        Pt 0 0 27.44 0
        Pt 0 3.92 27.44 3.92
        Pt 0 7.84 27.44 7.84
        Pt 1.96 -5.88 27.44 6.198064214
        Pt 1.96 -1.96 27.44 2.771858582
        Pt 1.96 1.96 27.44 2.771858582
        Pt 1.96 5.88 27.44 6.198064214
        Pt 3.92 -3.92 27.44 5.543717165
        Pt 3.92 0 27.44 3.92
        Pt 3.92 3.92 27.44 5.543717165
        Pt 5.88 -1.96 27.44 6.198064214
        Pt 5.88 1.96 27.44 6.198064214
        Pt 7.84 0 27.44 7.84
        Pt -5.88 -3.92 29.4 7.0668805
        Pt -5.88 0 29.4 5.88
        Pt -5.88 3.92 29.4 7.0668805
        Pt -3.92 -5.88 29.4 7.0668805
        Pt -3.92 -1.96 29.4 4.382693236
        Pt -3.92 1.96 29.4 4.382693236
        Pt -3.92 5.88 29.4 7.0668805
        Pt -1.96 -3.92 29.4 4.382693236
        Pt -1.96 0 29.4 1.96
        Pt -1.96 3.92 29.4 4.382693236
        Pt 0 -5.88 29.4 5.88
        Pt 0 -1.96 29.4 1.96
        Pt 0 1.96 29.4 1.96
        Pt 0 5.88 29.4 5.88
        Pt 1.96 -3.92 29.4 4.382693236
        Pt 1.96 0 29.4 1.96
        Pt 1.96 3.92 29.4 4.382693236
        Pt 3.92 -5.88 29.4 7.0668805
        Pt 3.92 -1.96 29.4 4.382693236
        Pt 3.92 1.96 29.4 4.382693236
        Pt 3.92 5.88 29.4 7.0668805
        Pt 5.88 -3.92 29.4 7.0668805
        Pt 5.88 0 29.4 5.88
        Pt 5.88 3.92 29.4 7.0668805
        Pt -7.84 0 31.36 7.84
        Pt -5.88 -1.96 31.36 6.198064214
        Pt -5.88 1.96 31.36 6.198064214
        Pt -3.92 -3.92 31.36 5.543717165
        Pt -3.92 0 31.36 3.92
        Pt -3.92 3.92 31.36 5.543717165
        Pt -1.96 -5.88 31.36 6.198064214
        Pt -1.96 -1.96 31.36 2.771858582
        Pt -1.96 1.96 31.36 2.771858582
        Pt -1.96 5.88 31.36 6.198064214
        Pt 0 -7.84 31.36 7.84
        Pt 0 -3.92 31.36 3.92
        Pt 0 0 31.36 0
        Pt 0 3.92 31.36 3.92
        Pt 0 7.84 31.36 7.84
        Pt 1.96 -5.88 31.36 6.198064214
        Pt 1.96 -1.96 31.36 2.771858582
        Pt 1.96 1.96 31.36 2.771858582
        Pt 1.96 5.88 31.36 6.198064214
        Pt 3.92 -3.92 31.36 5.543717165
        Pt 3.92 0 31.36 3.92
        Pt 3.92 3.92 31.36 5.543717165
        Pt 5.88 -1.96 31.36 6.198064214
        Pt 5.88 1.96 31.36 6.198064214
        Pt 7.84 0 31.36 7.84
        Pt -5.88 -3.92 33.32 7.0668805
        Pt -5.88 0 33.32 5.88
        Pt -5.88 3.92 33.32 7.0668805
        Pt -3.92 -5.88 33.32 7.0668805
        Pt -3.92 -1.96 33.32 4.382693236
        Pt -3.92 1.96 33.32 4.382693236
        Pt -3.92 5.88 33.32 7.0668805
        Pt -1.96 -3.92 33.32 4.382693236
        Pt -1.96 0 33.32 1.96
        Pt -1.96 3.92 33.32 4.382693236
        Pt 0 -5.88 33.32 5.88
        Pt 0 -1.96 33.32 1.96
        Pt 0 1.96 33.32 1.96
        Pt 0 5.88 33.32 5.88
        Pt 1.96 -3.92 33.32 4.382693236
        Pt 1.96 0 33.32 1.96
        Pt 1.96 3.92 33.32 4.382693236
        Pt 3.92 -5.88 33.32 7.0668805
        Pt 3.92 -1.96 33.32 4.382693236
        Pt 3.92 1.96 33.32 4.382693236
        Pt 3.92 5.88 33.32 7.0668805
        Pt 5.88 -3.92 33.32 7.0668805
        Pt 5.88 0 33.32 5.88
        Pt 5.88 3.92 33.32 7.0668805