On Sat, Jun 19, 2010 at 10:46 AM, Egon Willighagen <
egon.willigha...@gmail.com> wrote:
> Hi Bob,
>
> On Sat, Jun 19, 2010 at 5:39 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> >> * it took me a few minutes to realize how to unset the 'delete atom'
> mode
> >
> > Suggestions? My original plan was to have icons with the selections, so
> that
> > the top icon would change to reflect what was selected in the
> subdirectory.
>
> My first intuition was to click the item again... since it was a
> checkbox, that's what I would have expected... it could default to the
> 'C' mode again... or whatever the default action for the 'Model Kit'
> is...
>
>
Ah, yes. Well, I couldn't get radio buttons to work....
> >> * it would be nice if the FF energy would be displayed somewhere
> >
> > I experimented with that a bit, but because UFF is not reliable in terms
> of
> > energy, I thought it unwise to go there.
>
> Ah, but then again, you are using it for minimization... anyway, I was
> using it to compare to possible geometries... and UFF energies were
> pretty close, which was enough for me...
>
>
The magnitudes are off, if not the general trends.
> >> * the edit modes are quite hidden now, in the popup menu, so that
> >> changing drawing mode takes quick a few clicks
> >
> > true. Suggestions?
>
> Toolbar?
>
Applet?
>
> >> * changing an atom symbol of an existing atom could benefit from
> >> keyboard shortcut. I suggest that when an atom is highlighted (red
> >> circle), clicking 'C' changes to carbon, etc.
> >>
> > certainly sounds reasonable. What about Br? Cl? Can't buffer the atoms
> > because the idea is that it automatically adjusts H atoms. Or shouldn't
> it
> > do that?
>
> I think Rich Apodaca's 2D editor has the right approach... it keeps a
> time out, and if "b .. r" is typed within a certain time limit, it is
> Br...
>
>
Interesting idea.
> >> But the biggest issue by far was that I could not export the generator
> >> model in anything but .spt... :) I can easily extract the MDL molfile
> >> content from that, and realize Bioclipse should really support Jmol
> >> .spt files :)
> >
> > I'm saving MOL files from that third "..." menu. Does that not work for
> you?
>
> Oh, had not seen that :(
>
> Well, that's actually another point... it seems pretty remote from the
> actual GUI (or at least in the application)... I was really expecting
> a File -> Save As ...
>
> sure. could do that. I think the menu has lots of room for improvement.
Mainly I just wanted something functional and not too complicated.
> Egon
>
> --
> Post-doc @ Uppsala University
> Proteochemometrics / Bioclipse Group of Prof. Jarl Wikberg
> Homepage: http://egonw.github.com/
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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