2008/4/6, Park Won-Kyu <[EMAIL PROTECTED]>: > 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) >
finally I know the correct method :) "connect (atomindex=<from>) (atomindex=<to>)" atomindices are zero based index but atomnos are named tag (It is not documented yet.. :( ) and I made a quick hacked patch to "move atoms and add atoms" http://chemie.skku.ac.kr/jmol2.html ALT +Left mouse drag action move a atom CTRL + Left mouse drag action add a atom ( a Carbon) and also you can add H,O,N,S etc. by press "C" key on the applet This is a very dirty patch but you can see the basic idea from it. Regards, Won-Kyu Park
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