I have looked at it a little more. Turns out that the exported structures do load into JSmol (…. 06.30) with the odd exception of the .spardir. It will load by dropping it one the JSmol window, but will not with the load local file. For that I get a “no atoms found” error. That is true of the structure I was working with and with n-hexane. A file reading glitch in the load sequence?
> On Jul 19, 2016, at 12:19 PM, Otis Rothenberger <osrot...@icloud.com> wrote: > > 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 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
