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 ri

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 selection

[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 -