Hi, with Jmol 12.0 you can use the following Jmol Script command:
load SMILES "Oc1ccc(cc1)C3(OC(=O)c2ccccc23)c4ccc(O)cc4" (see: http://chemapps.stolaf.edu/jmol/docs/?&fullmanual=1&ver=12.0#k428 ) That works for me with the Application. On a webpage you probably need to use the signed Applet. (see: http://jmol.sourceforge.net/jslibrary/#jmolInitialize ) Oliver On Tue, Aug 17, 2010 at 01:46, John Francis Lee <[email protected]> wrote: > Worked like a charm! Thanks. > > I went to the website, pasted the SMILES string into a box labeled > SMILES and up popped the structure! > > Then I chose XYZ under download and downloaded the file. > > I opened jMol and then opened the file I downloaded and voila... the > molecule magically appeared. > > I wonder if I could do that in that in a browser window? > > If I knew the SMILES string for a given molecule could I send an http > GET to the cdb.ics.uci.edu server and get back a file the jMol applet > could read and display? > > On 08/17/2010 02:25 PM, Maurice Schroff wrote: >> Dear Mr. Lee >> >> As Jmol is a sort of "molecule viewer" it has no possibility to model >> molecules. However you can search various of pre-modeled molecules e.g. at >> http://cdb.ics.uci.edu/cgibin/ChemicalSearchWeb.psp . Jmol can read >> different formats including.xyz, .mol , .mol2 and .pdb >> Alternatively you could try to model using ChemDraw or Freeware as >> ACD/ChemSketch >> >> Regards, >> Maurice >> >> -----Ursprüngliche Nachricht----- >> Von: John Francis Lee [mailto:[email protected]] >> Gesendet: Dienstag, 17. August 2010 08:50 >> An: [email protected] >> Betreff: [Jmol-users] How to create jmol models >> >> Hi, >> >> Let me just blurt out my question : how can I make jmol models of molecules? >> >> Say I go to wikipedia and look up phenolphthalein. There I find >> >> IUPAC name : 3,3-bis(4-hydroxyphenyl)isobenzofuran-1(3H)-one >> CAS number : 77-09-8 >> SMILES : Oc1ccc(cc1)C3(OC(=O)c2ccccc23)c4ccc(O)cc4 >> >> Is any or all of this sufficient to model phenolphthalein in jmol? >> >> I looked at the wiki, expecting to find a whole section on how to do this, >> but I didn't recognize the instructions for doing so, if they're there. >> >> Thanks for any help you might give me. ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
