Angel, sorry to confuse, CHIME was able to display a flat version of a 2D file where all z coords were 0.0 There was an extra piece of code in the commercial version that allowed some energy minimisations and movement of atoms around and then to re-minimise. Its been a while since I played with it.
SCULPT...Automatic molecule conversion from 2D to 3D when pasting from 2D drawing programs that support the MDL Mol format Re SMILES, note that the JME generates a different SMILES string to say ChemAxon. For many years we have had a 1st year tutorial where we provide them with formulae and tell the students to draw the structures and these are graded by comparing the known SMILES with what JME calculates. We had a second version using the ChemZxon programmes and had to redo all the SMILES strings since they were not the same. The quizzes were for simple alkyls, more complicated alkyls and aryls and substituted species with chiral centres etc. The web pages are behind our campus firewall so not publicly accessible and it is now being maintained by a colleague in the Organic Chem section. Works like a charm... Robert Prof. Robert J. Lancashire mailto:robert.lancash...@uwimona.edu.jm Department of Chemistry Tel (876) 512 3026 University of the West Indies, Kingston 7 Fax (876) 977 1835 Mona Campus, JAMAICA. http://wwwchem.uwimona.edu.jm/chrl.html ________________________________________ Message: 1 Date: Thu, 29 Apr 2010 12:03:32 +0200 From: Angel Herr?ez <angel.herr...@uah.es> Subject: Re: [Jmol-developers] 2D/3D project To: <jmol-developers@lists.sourceforge.net> Message-ID: <4bd95974.31731.5c2...@angel.herraez.uah.es> Content-Type: text/plain; charset="US-ASCII" A few comments: 1. JCP has the advantage of accepting SMILES; which I think is more widespread and feature-loaded than JME. I also allows more variety when drawing structures. I have set quizzes that use SMILES to match user-drawn structures against correct answers. I doubt that JME string would be capable of not too simple structures. (I may be wrong in my appreciation of JME capabilities) 2. I think that MOL is a better choice for inter-app transfer than JME 3. Re. JME specification: some hints at http://wiki.jmol.org/index.php/File_formats/Coordinates#JME ------------------------------ Message: 2 Date: Thu, 29 Apr 2010 12:05:31 +0200 From: Angel Herr?ez <angel.herr...@uah.es> Subject: Re: [Jmol-developers] Jmol-developers Digest, Vol 47, Issue 6 To: <jmol-developers@lists.sourceforge.net> Message-ID: <4bd959eb.19828.5df...@angel.herraez.uah.es> Content-Type: text/plain; charset="ISO-8859-1" Robert, do you mean that Chime would do 3D starting from a flat structure? I've never seen that El 28 Apr 2010 a las 17:34, LANCASHIRE,Robert J escribi?: > this would then mean Jmol really does provide a replacement for MDL CHIME..... > Would Jmol then read mol files where all the z coords were zero and be able > to generate a reasonable representation? ------------------------------------------------------------------------------ _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
