[Jmol-users] Jmol Wiki

Hi, I've successfully created an accounton Jmol wiki using my institutional email and confirmed it now I'm wondering how am I meant to edit my User page or can't I do so as I see no "Edit this page" tab appearing for my user page. Thanks for your time,

[Jmol-users] AtomNo AtomIndex Issue

Bob, In a sequence of model editing operations involving the following, I end up with some atomno/atom-index confusion. The editing steps are: 1) Model bond change. 2) Model duplication. 3) Single model delete. After this sequence, atomno seems to lose its mathematical relationship to atom ind

[Jmol-users] Buckyball and UFF

Dear Jmol users, I loaded a single xyz structure of C60 into Jmol (older and latest versions), in order to extract UFF intramolecular bonding parameters. Thanks to an older post from Bob, this was an easy step : set loglevel 6 minimize steps 0 x = script("show minimization") print x set debug off

Re: [Jmol-users] Buckyball and UFF

It's certainly possible in JavaScript; less so in Java. In jsmol/j2s/JM/ff/UFF.txt change atom [c] C_R aromatic C to atom [#6] C_R aromatic C This will cause ALL carbons to be aromatic, so don't leave it like this! Bob On Mon, May 5, 2014 at 1:31 PM, Jenheta da

Re: [Jmol-users] AtomNo AtomIndex Issue

Beware of using atomIndex and atom/model deletion. When deleting atoms, atomIndex is not changed. There are just some missing. When a model is deleted, whole sections of the model atom array are excised, and all objects referring to atoms by atom number are recreated. However, there is a bug. Usi

Re: [Jmol-users] AtomNo AtomIndex Issue

this is fixed. On Mon, May 5, 2014 at 5:13 PM, Robert Hanson wrote: > Beware of using atomIndex and atom/model deletion. > > When deleting atoms, atomIndex is not changed. There are just some missing. > When a model is deleted, whole sections of the model atom array are > excised, and all objec