If your model has double bonds and hydrogens, that should work unless the
guanidine is part of an aromatic ring.
If your model does not have double bonds or hydrogens, you need:
select substructure("[N][CD3]([N])[N]")
If your model MIGHT have double bonds, you need:
select substructure("[N][CD3]([N])~[N]")
to allow for one double bond.
If the guanidine might be part of an aromatic system, you can use:
select substructure("/noaromatic/[N][CD3]([N])~[N]")
Except for the /noaromatic/ part, this is standard SMILES notation.
Bob
On Thu, Feb 6, 2014 at 6:22 AM, Ivan Pavicevic <[email protected]> wrote:
> Dear Jmol group,
> I'm using Jmol several years and I think that Jmol is the best
> solution for pdb visualization on my slackware linux system. But,
> yesterday I faced a problem when I tried to select all free guanidino
> and amino groups. I have found, in the wiki, and then figured out that
> select substructure("NC(N)=N") should worked, but Jmol selected 0
> atoms. Can you help me to solve this problem?
> Thanks,
> Ivan
>
> --
> If you don't care where you are, then you ain't lost
>
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
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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