also, there's a bug that I just fixed -- you need to use search(), not
substructure().
On Thu, Feb 6, 2014 at 6:54 AM, Robert Hanson <[email protected]> wrote:
> 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
>
>
--
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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Take advantage of what the Cloud has to offer - Avoid Common Pitfalls.
Read the Whitepaper.
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