[Jmol-users] Re: Jmol with lone pair

[Miguel <mt...@mt...>]

> I met another issue. How to add lone pairs of electrons to Jmol.
Scott,

Unfortunately, I have *no* idea what a "lone pair" is ... I am a computer
guy, not a chemist :)

Perhaps someone else can help out on this issue.

>
> My first thought is that I can add another new atom to the .cml file to
> simulate the lone pairs. The issue is that I need to change the new atom
> to ballon shaped, semi transparent grey, with a fuzzy edge. Is this
> feasible? My guess it should be a possible to change the shape of "LP"
> atom, could you please enlighten me?
>
>
> The methanol1.cml
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------
> --------
> <?xml version="1.0" encoding="ISO-8859-1"?>
> <!DOCTYPE molecule SYSTEM "cml.dtd" []>
> <molecule id="METHANOL">
>   <atomArray>
>      <stringArray builtin="id">a1 a2 a3 a4 a5 a6 a7</stringArray>
>      <stringArray builtin="elementType">C O H H H H LP</stringArray>
> <floatArray builtin="x3" units="pm">-0.748 0.558 -1.293 -1.263
> -0.699 0.716 0.99</floatArray>
>      <floatArray builtin="y3" units="pm">-0.015 0.420 0.202 0.754 -0.934
> 1.404 0.99</floatArray>
>      <floatArray builtin="z3" units="pm">0.024 -0.278 -0.901 0.600 0.609
> 0.137 0.99</floatArray>
>   </atomArray>
> </molecule>
> ------------------------------------------------------------------------
> ------------------------------------------------------------------------
> -----------
>
> You can see the applets from here
> http://128.233.95.77:2003/webdav/jmol.htm
> <http://128.233.95.77:2003/webdav/jmol.htm>
>
>
> Thanks
>
>
> Scott Zhao
> Programmer Analyst
> Educational & Research Technology Services
> Information Technology Services Division
> University of Saskatchewan
> Telephone: (306) 966-2395
> Fax: (306) 966-4938
>
>