Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

e but could be misleading. >> >> Otherwise works nicely. >> >> >> All the best >> Nick >> -- >> 3D Organic Animations http://www.chemtube3d.com >> Tel: +44 (0)151-794-3506 (3500 secretary) >> >> >> Subject: [

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

ir, >> biphenyl is flat, simple amides are not planar. This is not Jmol's fault per >> se but could be misleading. >> >> Otherwise works nicely. >> >> >> All the best >> Nick >> -- >> 3D Organic Animations http:

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

nstead of chair-chair, > biphenyl is flat, simple amides are not planar. This is not Jmol's fault per > se but could be misleading. > > Otherwise works nicely. > > > All the best > Nick > -- > 3D Organic Animations http://www.chemtube3d.com > Tel:

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

Oops, I missed an important point. I just checked Peter Ertl's documentation. There is also a molfile string reader function: readMolFile(String molFile) Otis On 4/12/2010 12:09 PM, Robert Hanson wrote: So to get JME to read files, just have Jmol read the file and pass the string to JME.

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

So to get JME to read files, just have Jmol read the file and pass the string to JME. JME.readMolecule(jmolEvaluate('load('" + filename + '")')) Bob On Mon, Apr 12, 2010 at 11:01 AM, Otis Rothenberger wrote: > Bob, > > I think it only reads strings. Implied in your note is the use of the > foll

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

Bob, I think it only reads strings. Implied in your note is the use of the following JME function via Live Connect: readMolecule(JME String) The set minimizationSilent is a big plus. Thank you for that one. I'll need to get the latest version to check it out, but it sounds like the molecular

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

sorry -- meant to respond there... Nick - that is a perfectly good point. Obviously a 2D representation is ambiguous with regard to conformation. So that's a limitation. I've put in some minimal checks, but it is still going to be an issue. Particularly with cyclohexane conformations you might get

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

.chemtube3d.com > Tel: +44 (0)151-794-3506 (3500 secretary) > > > Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D > To: jmol-users@lists.sourceforge.net > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" >

[Jmol-users] well, what do you know? Jmol and JME 2D to 3D

e but could be misleading. Otherwise works nicely. All the best Nick -- 3D Organic Animations http://www.chemtube3d.com Tel: +44 (0)151-794-3506 (3500 secretary) Subject: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D To: jmol-users@lists.sourceforge

Re: [Jmol-users] well, what do you know? Jmol and JME 2D to 3D

Very nice indeed! Bob, you are close to forcing me to upgrade the version of Jmol I am now using. Bill On Apr 11, 2010, at 12:52 AM, Robert Hanson wrote: OK! Here we go! Super simple 2D to 3D. The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5 addition of rea

[Jmol-users] well, what do you know? Jmol and JME 2D to 3D

OK! Here we go! Super simple 2D to 3D. The JME-Jmol connection has gone unused for too long. With today's 12.0.RC5 addition of reading bond stereochemistry, Jmol now does a pretty decent job of translating 2D into 3D -- admittedly this is not going to solve all problems, but give it a try: http:/