I was intrigued by the structure of the macrolide rapamycin after reading the article in C&EN yesterday. So I went after the 3-D structure.
I could not find it in any of the databases used by standard JSmol so I went off the Wikipedia and copied the smiles and inche strings. Using the console I was able to load from the smiles string, though the image was flat. Thinking Spartan would be faster at minimization, I exported from JSmol as a mol file which I loaded into Spartan and minimized. It was fast, but the result was ridiculous; a part of the molecule threaded through the macrocycle. I went back to JSmol and used the minimization function to begin a 3-D structure. I did not let it go to completion, but exported it as a mol file to load into Spartan. Spartan minimized it. I saved it as Spartan directory and as a mol file. For the mol file I was told that there were 8 unidentified atoms that were counted as dummy atoms. Neither would load into JSmol. It takes a while, but JSmol minimizes the structure to something reasonable. I then tried to load the inche string from the JSmol console using load inche “string”. Got a load error. What is the proper syntax for this and what is going on with Spartan?? Phil Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
