Phil, Resolver is string entry “smart,” so you can use load $IDENTIFIER from the console or a script. You might need the InChI= in the IDENTIFIER string. When I tried this, it was flat!
While CORINA docs state that there is no atom limit, you have to get through CORINA’s ensemble creation front door. I suspect, that this step is failing with the return of the 2D. Recall that CORINA needs to break molecules into known ensembles which are then reassembled as 3D. FYI, CORINA DOCS. I have no clue what’s going on in SPARTAN. Otis -- Otis Rothenberger o...@chemagic.org http://chemagic.org > On Jul 19, 2016, at 11:49 AM, Philip Bays <pb...@saintmarys.edu> wrote: > > 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 ------------------------------------------------------------------------------ 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
