I also thank to Jmol Dev Team!! 2008/4/4, Angel Herráez <[EMAIL PROTECTED]>: > So I've being playing for a few days with the minimization of structures in > Jmol, and I'm very > happy with the result; I think it will make an excellent educational tool. > I'm feeding Jmol with > 2D structures drawn and then exported into MOL format. >
I think the combination of the JME + Jmol is the possible one. (WebMO(?) already have a 2D->3D feature) > (All this runs within a single web page, though I'm not ready yet to go > public with it.) > > One thing I miss, and would be interesting to have, but likely not trivial > to implement, is > retention of the stereochemistry. > Despite being 2D, formula drawing programs allow to put wedge bonds > (up/down), and at > least JChemPaint exports them correctly into MOL format. However, since the > Z coordinate > is zero for all atoms, that stereo info is lost. > and then.. *moving atom* feature might be needed ... and there was already some patch exists in the Bug tracking system by me. (PR #1830352) http://sourceforge.net/tracker/index.php?func=detail&aid=1830352&group_id=23629&atid=379135 (The nanoCAD already have this *moving atom* feature) http://server.ccl.net/cca/software/SOURCES/JAVA/ncad/unpacked/ncad.html and the PR #1830352 implement *moving atom* with ALT + mouse LEFT button. > I can think of a way to set some positive or negative Z value on each atom > depending on > the type of stereo bond (even using Javascript) and so modifiy the MOL > before giving it to > Jmol, but then I'd need that Jmol retains that configuration, which it is > not doing right now > upon minimization. > > I realize the implications for the calculation are heavy, and it may even be > undesirable to > have it active by default --could be a toggle option--. > maybe smaller step limitaion needed by default. > Any insights? > BTW I realize that the *adding atom* feature already implemented by "data" command with some script flag e.g) set appendnew false; data "append mymol" 1 C 0.0 0.0 1.0 end "append mymol connect (atomno=<from no>),(atomno=<to num>) BUT I found that this feature is not working correctly. (svn version) ..... :( ( load append "test.cif" works fine but *data* command does not) Thanks for this great software :> Regards Won-kyu Park ------------------------------------------------------------------------- This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Register now and save $200. Hurry, offer ends at 11:59 p.m., Monday, April 7! Use priority code J8TLD2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
