VMD-L Mailing List

From: Paul Fons (paul-fons_at_aist.go.jp)
Date: Tue Oct 21 2003 - 01:52:22 CDT

I have been using vmd for looking at small inorganic clusters and I had
what I hope is a trivial question about bonds. I understand (and am
using the concept of dynamic bonds), but I would like to be able to
specify a set of bonds to be drawn. I thought the PDB file format
allowed this. When I tried to specify bonds using the input below,
dynamic bonds are calculated (actually I scaled the data so they
wouldn't be drawn as I don't know how to turn this feature off), but my
bond specifications seem to be ignored. Any idea of what I am doing
incorrect?

COMPNDMSC_CIF_
REMARK THIS FILE GENERATED BY P.Fons
ATOM 1 Ge X 1 -5.710 -5.710 0.000 0.00 0.00
ATOM 2 Te X 1 0.000 -5.710 0.000 0.00 0.00
ATOM 3 Sb X 1 5.710 -5.710 0.421 0.00 0.00
ATOM 4 Te X 1 0.000 0.000 -6.020 0.00 0.00
ATOM 5 Te X 1 12.040 -6.020 0.000 0.00 0.00
ATOM 6 Te X 1 6.020 0.000 0.000 0.00 0.00
ATOM 7 Ge X 1 5.710 5.710 0.421 0.00 0.00
ATOM 8 Te X 1 6.020 6.020 6.020 0.00 0.00
ATOM 9 Te X 1 0.000 5.710 0.000 0.00 0.00
ATOM 10 Sb X 1 -5.710 5.710 0.421 0.00 0.00
ATOM 11 Te X 1 -6.020 0.000 0.000 0.00 0.00
ATOM 12 Te X 1 0.000 0.000 6.020 0.00 0.00
CONECT 1 11 1
CONECT 2 1 4
CONECT 4 2 6 5
CONECT 5 4
CONECT 6 4 7
CONECT 7 6 9
CONECT 8 7
CONECT 9 7 10
END

Paul Fons, Ph.D.
Senior Staff Researcher
Photonics Institute
National Institute for Advanced Industrial Science & Technology
Umezono 1-1-1
Tsukuba Central 2
Tsukuba, JAPAN 305-8568
email: paul-fons_at_aist.go.jp
tel. +81-298-61-5636 fax: +81-298-61-5615
http://staff.aist.go.jp/paul-fons
The lines below are in Japanese
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