Hi Otis,
 
your solution sounds very good.Exactly what I'm looking for.
 
But it does not work within the Wiki-Extension. I tried
select *;if ({atomno < 10}.partialcharge == 0){calculate partialcharge;}isosurface resolution 0 vdw color range -.07 .07 map mep translucent;
and
select *; calculate partialcharge; isosurface resolution 0 vdw color range -.07 .07 map mep translucent;
in a localy installed Jmol and it works nice.
 
But in the Wiki the first script causes an error, when saving the Wiki-Page:  XML error: XML_ERR_NAME_REQUIRED at line 5
with this Wiki-Code:
 
== Test ==
<jmol>
 <jmolApplet>
 <size>300</size>
 <uploadedFileContents>Formaldehyd.cml</uploadedFileContents>
<script>select *;if ({atomno < 10}.partialcharge == 0){calculate partialcharge;}isosurface resolution 0 vdw color range -.07 .07 map mep translucent</script>
 </jmolApplet>
</jmol>

And with the shorter code I did not get an error but no effect!
 
Does anybody knows if the Wiki-Extension does support the MEP-calculation? Or is it may be an old version?
 
Thanks in advance, Birgit
 
 
 
 
 

> Otis Rothenberger <osrothen@chemagic.com> hat am 25. April 2013 um 21:45 geschrieben:
>
>
> Hi Birgit,
>
> Jmol can calculate MMFF94 partial charges. The following script may be more complex than you need. It first checks to see if your file has partial charges. If it does not, then the MMFF94 charges are calculated. The MEP is then displayed:
>
> select *;if ({atomno < 10}.partialcharge == 0){calculate partialcharge;}isosurface resolution 0 vdw color range -.07 .07 map mep translucent
>
> Otis
>
> --
> Otis Rothenberger
> otis@chemagic.com
> http://chemagic.com
>
>
>
>
> On Apr 25, 2013, at 2:22 PM, birgit@lachner-net.de wrote:
>
> > Hi everybody,
> >
> > best wishes from germany and thanks a lot specially to the develloper. I'm chemistry-teacher in germany and use the Wiki-extension to create interactive pictures for my pupils. Look for example at the page http://wikis.zum.de/chemie-digital/Frau_Lachner/Was_die_Siedetemperatur_von_Molek%C3%BClen_beeinflusst#Van_der_Waals-Kr.C3.A4fte.
> > I managed it to use little scripts and buttons even if the informations for the extensions are not so clear and easy.
> >
> > I'm new to the list because I wanted to show the electrostatic potential of a molecule on its surface. There are of cause some informations on the help pages for scripting. As far as I understand the help-text, Jmol can not calculate it on its own but only show it, if it is given in a file.
> >
> > But I do not understand how to get such a file? What kind of software is needed?
> >
> > As Linux-User I use Avogadro to draw the molecules. And Avogadro can calculate the electrostatic potential. Can I save the calculations from Avogardo?
> >
> > Best regards and thanks for your efforts, Birgit
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