Thanks Bob! Works :) Now I realize that I have misunderstand concept of substructure() procedure, and treated "SMILES" strings with copy/paste philosophy. Jmol is awesome. Cheers, Ivan
On Thu, Feb 6, 2014 at 1:54 PM, 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 >> >> >> ------------------------------------------------------------------------------ >> Managing the Performance of Cloud-Based Applications >> Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. >> Read the Whitepaper. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk >> _______________________________________________ >> Jmol-users mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > -- > 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 > > > ------------------------------------------------------------------------------ > Managing the Performance of Cloud-Based Applications > Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. > Read the Whitepaper. > http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-users mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- If you don't care where you are, then you ain't lost ------------------------------------------------------------------------------ Managing the Performance of Cloud-Based Applications Take advantage of what the Cloud has to offer - Avoid Common Pitfalls. Read the Whitepaper. http://pubads.g.doubleclick.net/gampad/clk?id=121051231&iu=/4140/ostg.clktrk _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
