You would attach a 3D echo rather than a label.
use a SMARTS search for SS:
Var ssBondAtoms = {*}.find("SMARTS","SS")
Then get those bonds:
Var ssBonds = ssBondAtoms.bonds
Now go through those, pinpointing the centers:
for (Var i = 1; i <= ssBonds.length; i++) {
Var bondCenter = ssBonds[i].xyz
script inline @{"set echo ssbond" + i +" " + bondCenter + ";echo
WHATEVER"}
}
[The script inline business is necessary because I have not gotten set echo
going with variables yet .]
Bob
On Thu, Apr 14, 2011 at 3:00 AM, <jaime.prilu...@weizmann.ac.il> wrote:
>
> A question just came out from a chemistry teachers workshop:
> "Can you place a label pointing to an ssbond?" They wanted to
> make it evident for students where hbonds and ssbonds are.
>
> My question: how do I select a particular (or all) ssbond/hbond ?
> The idea is not to select neither of the atoms that the
> bond is connecting to, but to the bond line itself.
> If possible, then, can I attach a label to the selection?
>
> Thanks in advance,
> Jaim
> --
> Dr Jaime Prilusky | jaime.prilu...@weizmann.ac.il
> Head Bioinformatics |
> R&D Bioinformatics and Data Management |
> Department of Biological Services |
> Weizmann Institute of Science | fax: 972-8-9344113
> 76100 Rehovot - Israel | tel: 972-8-9344959
>
> OCA, http://oca.weizmann.ac.il (the protein structure/function database)
> Proteopedia, http://proteopedia.org (because life has more than 2D)
> ------------------------------------------------------------------------
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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