[Jmol-users] SMARTS question
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
Re: [Jmol-users] SMARTS question
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 -- 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
Re: [Jmol-users] SMARTS question
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 > > > > -- > 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 > -- 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 -- 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