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 [email protected] ------------------------------------------------------------------------------ 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 [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
