Hi James,
Just to address your comment about the Avogadro crashing, it's a known
problem and is a prime motivator for a major rewrite of Avogadro that the
developers are currently undertaking.
You can read Marcus' announcement about Avogadro2 in his mail to this list
on the 11th April:
http://sourceforge.net/mailarchive/forum.php?thread_name=CAEZy%3DVEhD4OKEPWyWgHnGkRZ%2B_m3t31R-2zmdtV2MaNZgWy%3DAQ%40mail.gmail.com&forum_name=avogadro-devel
This will bring in a large number of improvements and changes to the code,
but a major one will be that the crashing (usually caused by bugs in the
openbabel library crashing the whole app), should be a thing of the past.
In my experience the Linux versions tend to be less prone to crashing then
the Windows ones, so you might try the latest Avogadro and see if that
improves things for you until enough of the functionality has been ported
to Avogadro2 to make it usable for you.
Best wishes,
Jens
On 28 June 2013 18:42, James <ja...@ryley.com> wrote:
> Hi,
>
> I've used Avogadro here and there because of its great interface. But, I
> can't rely upon it because it crashes for me *all the time*. Originally I
> thought it was only with large models, but recently I've been playing with
> models of less than 1000 atoms and it still happens. This is on Windows
> 7. I've scanned some of the recent threads and it looks like stability
> issues in 1.1.0 are known. Which leads me to 2 questions:
>
> Are the Linux versions more stable?
> Is another release planned any time soon to address stability?
>
> I love the interface - just want to be able to use it without constant
> fear of losing my most recent changes in a crash.
>
> On an unrelated note, one suggestion I have is to improve atom choice for
> bonding. I find that I bind to the wrong atom fairly often (maybe it's just
> me!). Normally I bind to something which is behind the atom I intended, and
> if the angle is bad, it can even be hard to see you made a mistake. I think
> there are several ways to address this, such as:
>
> 1) Make the "from" and "to" atom highlighting very obvious. Rather than
> just snapping the bond to the atom (which is hard to interpret with many
> atoms, and when there are atoms in front of, or behind, the atom of
> interest), make the atom change color, glow, dance... ;)
>
> 2) Have a preference for atoms that are in front. For example, if one atom
> partially occludes another atom, the atom in front gets some preference in
> the snap-to algorithm. If one atom totally occludes another atom, it is
> almost a certainty that the user means the atom in front. (Maybe the ideal
> algorithm takes into account how much overlap there is - but since these
> are rendering rather than model details, I'm not sure how available this
> information is). Yes, this would make it harder to bind to
> partially-occluded atoms, but how often is that really the intent? I tend
> to spin or zoom my model to make the atom(s) of interest very visible - but
> perhaps other people do not.
>
> Thanks for a nice piece of software!
> Sincerely,
> James
>
>
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