From: Otis R. <osr...@ch...> - 2010-09-03 05:01:22
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Bob, I thought the taxol problem with the gif generation that I referenced below was the aromatic lower case issue I asked about earlier. Now I think not. The Resolver has translated other Jmol smiles with lower case Kekule aromatics correctly. It definitely can create the gif for taxol when this is addressed directly in the Resolver Web page. When I look at the SMILES that Jmol creates for taxol, I get the following: print {*}.find('SMILES'); C12[C@](C)3[C@@H](O)C[C@@H]4[C@]15OC(C)=O.[C@@H]26[C@](O)7C(C)(C)C8=C(C)[C@H]9OC%10=O.C79.C%118C3=O.O%11C(C)=O.O6C%12=O.c%12%13=cc=cc=c%13.C5O4.[C@H](O)%10[C@@H]%14c%15=cc=cc=c%15.N%14C%16=O.c%16%17=cc=cc=c%17 Resolver produces: CC(=O)O[C@H]1C(=O)[C@]2(C)[C@@H](O)C[C@H]3OC[C@@]3(OC(C)=O)[C@H]2[C@H](OC(=O)c4ccccc4)[C@]5(O)C[C@H](OC(=O)[C@H](O)[C@@H](NC(=O)c6ccccc6)c7ccccc7)C(=C1C5(C)C)C I'm guessing that Resolver can't deal with the 2 digit ring (or fragment) closure notation - i.e % notation. Otis Otis Rothenberger chemagic.com On 9/2/2010 10:24 PM, Otis Rothenberger wrote: > The NIH Resolver will generate a gif image of the Lewis line structure > of a submitted SMILES. I ignored this feature because I thought it was > just another pretty little picture. Boy was I wrong! > > A JavaScript construct of the following form: > > var tempStr = "<img width='" + sz + "' height='" + sz + "' > src='http://cactus.nci.nih.gov/chemical/structure/" + escape(jmolSmiles) > + "/image' />"; > > sz = desired gif size > jmolSmiles = an evolving model kit mode model. > > When rendered the above gif not only has appropriate bond wedges. The > chiral carbons are conveniently labeled R or S > > If you want to see a quick demo of this, go to > > http://chemagic.com/web_molecules/script_page_large.aspx > > The default model will be just fine. Click The Molecular Editor Link; > click the Image link, click the NIH 2D Capture link. > > We edit models using our own Edit screen interface rather than the Jmol > native interface. Play with editing, and you'll see that Resolver gets > it right. You need to click the image capture link each time. > > There are some problems with complex aromatics (e.g. taxol), but I'm > working on this problem. > > Otis > |