From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Oct 24 2003 - 18:51:59 CDT

Paul,
  You can selectively create/delete bonds in VMD via Tcl or with
the Mouse menu item for doing so. The PDB reader in VMD currently
ignores the CONECT records since VMD was originally written for use
with large macromolecules for which the CONECT records are useless.
(5 digits max in the atom indices referenced by the CONECT records).
So, at present you'd need to write a Tcl script if you want precise
control over bonding in VMD, other than those provided by the distance
based bond search, or from an ancillary file such as a PSF file.

I plan to upgrade the PDB reader to handle CONECT records in the case
where there are a legal number of atoms (i.e. less than 99999) and when
it can be deteremined that the CONECT records are sane. (i.e. the PDB
file hasn't been altered by various editing operations thus messing
up indices etc. But this will have to wait until VMD 1.8.2 is out
the door, which should be very shortly now.

Let us know if you need help with the Tcl stuff etc.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Oct 21, 2003 at 03:52:22PM +0900, Paul Fons wrote:
> 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
> $Bk8)!!(B 305-8568
>

-- 
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