Avogadro 1.0

IMHO, Avogadro isn’t stable enough for production use, so it seems too hastily to release 1.0 on 4th of Jule.
I think Avogadro needs RC version. It should be maked with such quality to get all things working right, and I’m sure, I’ll be able to find several files which will crash it
There may be many hidden bugs in plenty of extensions, and one extension working badly can discriminate user against whole Avogadro
Also I think some time is needed to correct translations, to enlarge documentation. This things need much more time than it may seem.

On Jun 21, 2009, at 7:47 AM, Konstantin Tokarev wrote:

There may be many hidden bugs in plenty of extensions, and one
extension working badly can discriminate user against whole Avogadro
Also I think some time is needed to correct translations, to enlarge
documentation. This things need much more time than it may seem.

I agree the release should be pushed back, maybe to August?

  • We depend on fixes in OB v2.2.2, which isn’t yet released.
  • As you say, we need a lot of testing in each extension. I also don’t
    like seeing the crashes and hope we can fix things on Windows.
  • Documentation needs a LOT of work. Besides some screencasts from
    Jan, nothing has happened except my work. I can’t do it all.
  • Translations I think are actually in good shape. I’m sure you might
    want Russian to be 100%, but this our least problem. People will
    forgive an incomplete translation, but not a crash or bad documentation.

There was a big push as we hit the feature-freeze, but there’s not
much activity anymore. Plus, cryos is a little busy with family.

So let’s fix as much as possible and release another 0.9.x.
-Geoff

On Sun, Jun 21, 2009 at 4:43 PM, Geoffrey
Hutchisongeoff.hutchison@gmail.com wrote:

On Jun 21, 2009, at 7:47 AM, Konstantin Tokarev wrote:

There may be many hidden bugs in plenty of extensions, and one
extension working badly can discriminate user against whole Avogadro
Also I think some time is needed to correct translations, to enlarge
documentation. This things need much more time than it may seem.

I agree the release should be pushed back, maybe to August?

Sounds good, especially documentation needs lots of work.

  • We depend on fixes in OB v2.2.2, which isn’t yet released.
  • As you say, we need a lot of testing in each extension. I also don’t
    like seeing the crashes and hope we can fix things on Windows.
  • Documentation needs a LOT of work. Besides some screencasts from
    Jan, nothing has happened except my work. I can’t do it all.

The work you have done looks good. I’ll work on a "selections"
tutorial tonight. It will probably be small explanations with short
youtube videos or screenshot to clarify.

  • Translations I think are actually in good shape. I’m sure you might
    want Russian to be 100%, but this our least problem. People will
    forgive an incomplete translation, but not a crash or bad documentation.

There was a big push as we hit the feature-freeze, but there’s not
much activity anymore. Plus, cryos is a little busy with family.

So let’s fix as much as possible and release another 0.9.x.
-Geoff


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Tim Vandermeersch wrote:

On Sun, Jun 21, 2009 at 4:43 PM, Geoffrey
Hutchisongeoff.hutchison@gmail.com wrote:

On Jun 21, 2009, at 7:47 AM, Konstantin Tokarev wrote:

There may be many hidden bugs in plenty of extensions, and one
extension working badly can discriminate user against whole Avogadro
Also I think some time is needed to correct translations, to enlarge
documentation. This things need much more time than it may seem.

I agree the release should be pushed back, maybe to August?

Sounds good, especially documentation needs lots of work.

Agreed.

  • We depend on fixes in OB v2.2.2, which isn’t yet released.
  • As you say, we need a lot of testing in each extension. I also don’t
    like seeing the crashes and hope we can fix things on Windows.
  • Documentation needs a LOT of work. Besides some screencasts from
    Jan, nothing has happened except my work. I can’t do it all.

The work you have done looks good. I’ll work on a "selections"
tutorial tonight. It will probably be small explanations with short
youtube videos or screenshot to clarify.

I am going to go through the tutorials I put up, update the screenshots
etc. I will make a new screencast showing off the new interface soon
too. I agree with Geoff that translations are in great shape, but the
extra time would be good to hunt down some of the bigger bugs we have in
Avogadro.

I am just about back to normal - the little guy is already helping me
out a little on the computer :wink:

Thanks,

Marcus

On Jun 22, 2009, at 2:28 PM, Tim Vandermeersch wrote:

The work you have done looks good. I’ll work on a "selections"
tutorial tonight. It will probably be small explanations with short
youtube videos or screenshot to clarify.

I think you and Marcus and Jan are doing the best videos. So I’m
generally staying away from that, but I think we need more static
walkthroughs too.

Thanks! I think we’ll have a great release when it’s done.
-Geoff

When importing crystal structure from CIF or RES, Avogadro takes information about bonds from OpenBabel interpretation. But sometimes its incorrect. It’ll be nice to have an apportunity to choose, what types of atoms can be conneted, and connect others if distances are acceptable. Such thing, for example, is implemented in proprietary program Diamond

On Jun 23, 2009, at 10:54 AM, Konstantin Tokarev wrote:

When importing crystal structure from CIF or RES, Avogadro takes
information about bonds from OpenBabel interpretation. But sometimes
its incorrect. It’ll be nice to have an apportunity to choose, what
types of atoms can be conneted, and connect others if distances are
acceptable. Such thing, for example, is implemented in proprietary
program Diamond

Can you outline this a bit more (particularly in comparison with
Diamond)? We have a section on the wiki for “inspiration” and you can
upload screenshots from other programs:

http://avogadro.openmolecules.net/wiki/Inspiration

Thanks,
-Geoff

Geoffrey Hutchison wrote:

On Jun 23, 2009, at 10:54 AM, Konstantin Tokarev wrote:

When importing crystal structure from CIF or RES, Avogadro takes
information about bonds from OpenBabel interpretation. But sometimes
its incorrect. It’ll be nice to have an apportunity to choose, what
types of atoms can be conneted, and connect others if distances are
acceptable. Such thing, for example, is implemented in proprietary
program Diamond

Can you outline this a bit more (particularly in comparison with
Diamond)? We have a section on the wiki for “inspiration” and you can
upload screenshots from other programs:

http://avogadro.openmolecules.net/wiki/Inspiration

This sounds like an extension of the super cell bonding I added. The
super cell builder takes a more simplistic view of bonding, and I have
been using this to guess the bonds in zeolite CIF files. We could
possibly break out the code and make it available to a file loader. It
would be great to see how Diamond approached exposing this functionality
to the user.

I am not totally clear on what adjustable parameters users would want to
see in a dialog for doing this. How useful would something like this be
to our user community?

It
would be great to see how Diamond approached exposing this functionality
to the user.
When use loads file, no atoms or bond are visible. Than, user clicks a button and selects, what elements may not be connected in molecule, e.g., H-H, N-N or C-Fe in aminocomplex of iron. Than al other atoms are automatically connected, if distances are short enough

On Jun 25, 2009, at 9:34 AM, Konstantin Tokarev wrote:

When use loads file, no atoms or bond are visible. Than, user clicks
a button and selects, what elements may not be connected in
molecule, e.g., H-H, N-N or C-Fe in aminocomplex of iron. Than al
other atoms are automatically connected, if distances are short enough

We could very easily have some sort of “re-assign bonding” command.
But what you’re describing is that you want to exclude certain atom
pairs from bonding?

-Geoff