I really appreciate your concern, thanks Bob! I have figured out another way to do-the-job with "select [ARG]:A.NH1 or [ARG]:A.NH2 or [ARG]:A.CZ or [ARG]:A.NE" Entire story was about sites accessible for chemical modifications in hyperglycemia, glycation sites, formation of Amadori products, etc. so just for visual purposes I think that I achieved results. :)
On Thu, Feb 6, 2014 at 3:17 PM, Robert Hanson <[email protected]> wrote: > 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 >>> >>> >>> ------------------------------------------------------------------------------ >>> 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 >> > > > > -- > 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
