VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 25 2001 - 13:39:35 CDT
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- In reply to: Mauricio Carrillo Tripp: "bond length definition"
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Dear Mauricio,
The default lengths used in the distance-based bond
search in VMD aren't currently controllable by the user, however this
suggestion is a good one (and one made by others previously) that we
intend to improve when time allows. The immediate solution to your problem
would be to:
1) use a structure file such as a PSF file, or use conect2psf to create one
if you're working with a PDB that has conect records.
or
2) use Tcl or Python scripts to allow you to interactively add or delete
bonds.
We intend to improve these mechanisms substantially, but our development
time is already maxed out with other activities, so it may be a while still.
(I have a large backlog of good things VMD should be doing that we haven't
had time to implement yet)
Thanks for using VMD!
John Stone
vmd_at_ks.uiuc.edu
On Tue, Apr 24, 2001 at 01:40:17PM -0500, Mauricio Carrillo Tripp wrote:
> Hi,
> Is there a way to define the bond length?
> I have a structure where two atoms are bonded,
> but vmd finds them too far away to each other and
> doesn't draw the bond. I looked in the manual, but
> couldn't find anything...
>
> thank you
>
> Mauricio C Tripp
> Biophysics Dept
> CCF-UNAM
> Mexico
-- NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801 Email: johns_at_ks.uiuc.edu Phone: 217-244-3349 WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
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