Re: [Jmol-users] SMARTS question

[Robert Hanson]

make sure you have loaded the file with

set pdbAddHydrogens

SMARTS is really not designed to work with models that do not indicate
bonding.

You  can also use Jmol BioSMARTS and target the sequences directly.




On Thu, Jun 29, 2017 at 12:28 PM, Eric Martz 
wrote:

> This selects the aromatic ring carbons of Phe and Tyr:
>
> rings6 = {*}.find("SMARTS","c1c1", true)
>
> It does not select the 6-atom ring of Trp.
>
> This selects the ring of His:
>
> ringsh = {*}.find("SMARTS","c1cncn1", true)
>
> How do I select the 5 and 6 atom rings of Trp?
>
> Thanks, Eric
>
>
> 
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-- 
Robert M. Hanson
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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Re: [Jmol-users] SMARTS question

[Kubasik, Matthew A.]

Eric,

I’ve not used SMARTS before, so I tried your commands below:

> rings6 = {*}.find("SMARTS","c1c1", true)
select rings6

and
> ringsh = {*}.find("SMARTS","c1cncn1", true)
select ringsh

Running the Jmol application, v. 14.8.0, and loading tryptophan via “load 
$tryptophan”, your selections do, indeed, identify tryptophan rings.

Not much help, but it seems to work in the app.

Matt




> On Jun 29, 2017, at 1:28 PM, Eric Martz  wrote:
> 
> This selects the aromatic ring carbons of Phe and Tyr:
> 
> rings6 = {*}.find("SMARTS","c1c1", true)
> 
> It does not select the 6-atom ring of Trp.
> 
> This selects the ring of His:
> 
> ringsh = {*}.find("SMARTS","c1cncn1", true)
> 
> How do I select the 5 and 6 atom rings of Trp?
> 
> Thanks, Eric
> 
> 
> --
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, Slashdot.org! http://sdm.link/slashdot
> ___
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users

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[Jmol-users] SMARTS question

[Eric Martz]

This selects the aromatic ring carbons of Phe and Tyr:

rings6 = {*}.find("SMARTS","c1c1", true)

It does not select the 6-atom ring of Trp.

This selects the ring of His:

ringsh = {*}.find("SMARTS","c1cncn1", true)

How do I select the 5 and 6 atom rings of Trp?

Thanks, Eric


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