VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Apr 08 2003 - 17:10:39 CDT

Dear Stephen,
  Can you email me (or vmd_at_ks.uiuc.edu, no need for all of VMD-L) the
specific error message you got? I assume you're running VMD 1.8 yes?
You cannot draw bonds between separate molecules in VMD, so if VMD
thought you were trying to do so, that might be relevent. The
automatic display of bonds in VMD has a lot do to with what type of
structure files you're working with. VMD will load bond info directly
from several file formats, but in other cases it uses a distance-based
bond search heuristic to guess them for itself. If you can tell us more
about what file format you working with, etc, that will help us determine
why you're not seeing what you expect.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Apr 08, 2003 at 04:37:08PM -0400, Stephen Koch wrote:
> I am interested in drawing bonds within an Fe4S4 cluster in a protein and
> between the cluster and S-Cys of the protein.
> I was confronted with the message that you cannot draw bonds between
> molecules. This occurred when I had the Fe4S4 cluster and the Cys's in
> different Graphical Representations. I would be desirable if the bonds
> involving transitions metals were automatically drawn.
>
> Stephen A. Koch 631-632-7944 (7931) Koch_at_sbchem.sunysb.edu Fax 631-632-7960
> Department of Chemistry, SUNY,Stony Brook, NY 11794-3400
> WWW: notes.cc.sunysb.edu/CAS/chemistry.nsf/pages/SKoch 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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