Avogadro 2 0.7.0 Released

Announcements
1

We are very proud to announce the availability of Avogadro 2 0.7.0.

Avogadro 2 is a free, open source, cross-platform molecular editor
designed for flexible use in computational chemistry, molecular
modeling, bioinformatics, materials science, and related areas.
Packages are available for Windows, Linux and Mac OS X. The source
code source is available under the 3-clause BSD license.

Avogadro 2 is a rewrite of Avogadro, and still lacks features present
in Avogadro 1. Both packages can be installed on the same system, and
so it is possible to try the latest without losing access to the
previous version. We will be making occasional releases of Avogadro
1.x too, along with migrating functionality to Avogadro 2. We value
your feedback, and hope that you will find the improvements made in
version 2 useful.

What does Avogadro 2 do?

  • We’ve tried to make the best, most intuitive “builder”
  • Interfaces to many common computational packages
  • Designed to help both educational users and advanced research
  • Plugins that allow it to be extended and customized
  • Can be extended with simple Python scripts for file IO and input generation
  • Well defined public API, libraries and modular design

Download: https://sourceforge.net/projects/avogadro/files/avogadro2/0.7.0/

What’s new? See the Release Notes: http://wiki.openchemistry.org/Avogadro2_0.7.0

For more information: http://wiki.openchemistry.org/Avogadro

If you use Avogadro or Avogadro 2, please check out the recently
published Avogadro paper, and consider citing it:

This is a community project and we couldn’t have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. We
acknowledge that the development of Avogadro 2 has been funded by a US
Army SBIR with the Engineering Research Development Center under
contract (W912HZ-12-C-0005) at Kitware, Inc.

2

I must say that, in my opinion, this release is premature. I appreciate the
comment ’ lacks features present in Avogadro 1’, but the new version appears
to be incapable of rendering benzene as a planar molecule at this point.
Although the optimized geometry of cyclohexane approximates the less stable
boat conformer, the 1.0 version will generate the more stable chair
conformer on optimization.

Is it possible that I am missing something in the new, more convoluted
directory and subdirectory structure of the gui?

Stephen P. Molnar, Ph.D. Life is a fuzzy
set
Foundation for Chemistry Stochastic and
multivariate
www.FoundationForChemistry.com
(614)312-7528 ©
Skype: smolnar1

-----Original Message-----
From: Marcus D. Hanwell [mailto:marcus.hanwell@kitware.com]
Sent: Monday, December 02, 2013 2:14 PM
To: Avogadro-devel Devel; avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

We are very proud to announce the availability of Avogadro 2 0.7.0.

Avogadro 2 is a free, open source, cross-platform molecular editor designed
for flexible use in computational chemistry, molecular modeling,
bioinformatics, materials science, and related areas.
Packages are available for Windows, Linux and Mac OS X. The source code
source is available under the 3-clause BSD license.

Avogadro 2 is a rewrite of Avogadro, and still lacks features present in
Avogadro 1. Both packages can be installed on the same system, and so it is
possible to try the latest without losing access to the previous version. We
will be making occasional releases of Avogadro 1.x too, along with migrating
functionality to Avogadro 2. We value your feedback, and hope that you will
find the improvements made in version 2 useful.

What does Avogadro 2 do?

  • We’ve tried to make the best, most intuitive “builder”
  • Interfaces to many common computational packages
  • Designed to help both educational users and advanced research
  • Plugins that allow it to be extended and customized
  • Can be extended with simple Python scripts for file IO and input
    generation
  • Well defined public API, libraries and modular design

Download: https://sourceforge.net/projects/avogadro/files/avogadro2/0.7.0/

What’s new? See the Release Notes:
http://wiki.openchemistry.org/Avogadro2_0.7.0

For more information: http://wiki.openchemistry.org/Avogadro

If you use Avogadro or Avogadro 2, please check out the recently published
Avogadro paper, and consider citing it:

This is a community project and we couldn’t have made this release without
you. Many thanks to all the contributors to Avogadro including those of you
who submitted feedback, bug reports, and code. We acknowledge that the
development of Avogadro 2 has been funded by a US Army SBIR with the
Engineering Research Development Center under contract (W912HZ-12-C-0005) at
Kitware, Inc.

–
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3

On Tue, Dec 3, 2013 at 8:25 AM, Stephen P. Molnar
s.molnar@sbcglobal.net wrote:

I must say that, in my opinion, this release is premature. I appreciate the
comment ’ lacks features present in Avogadro 1’, but the new version appears
to be incapable of rendering benzene as a planar molecule at this point.
Although the optimized geometry of cyclohexane approximates the less stable
boat conformer, the 1.0 version will generate the more stable chair
conformer on optimization.

I would disagree, and think that ‘release early, release often’ is a
useful mantra in closing the loop between development and use that is
employed by many open source projects (including Avogadro in the past,
and now). We worked hard to ensure you could install Avogadro 1 and 2
on the same machine, removing any requirement to choose one or the
other. Perhaps this article will fill add some of the motivation you
appear to be inquiring about,

http://www.kitware.com/source/home/post/113

When you say ‘incapable of rendering’ is this referring to the
forcefield optimization as your second point about cyclohexane is? I
am not sure I see any reason why a planar benzene would not render,
but could see the forcefield defaults giving issues. They both use the
same forcefields underneath (the ones developed by the Open Babel
project), and I can look into modifying our defaults as I had noticed
version 2 generally didn’t optimize the structures as well.

Is it possible that I am missing something in the new, more convoluted
directory and subdirectory structure of the gui?

It is, but you would have to be more specific for me to hope to answer
your question. If you are just interested in using the Avogadro
application I am not sure why this would concern you. Thank you for
your feedback, if you find Avogadro 2 unsuitable then certainly
continue using 1.1 for now - we have an update planned for that
shortly too.

Sincerely,

Marcus

-----Original Message-----
From: Marcus D. Hanwell [mailto:marcus.hanwell@kitware.com]
Sent: Monday, December 02, 2013 2:14 PM
To: Avogadro-devel Devel; avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

We are very proud to announce the availability of Avogadro 2 0.7.0.

Avogadro 2 is a free, open source, cross-platform molecular editor designed
for flexible use in computational chemistry, molecular modeling,
bioinformatics, materials science, and related areas.
Packages are available for Windows, Linux and Mac OS X. The source code
source is available under the 3-clause BSD license.

Avogadro 2 is a rewrite of Avogadro, and still lacks features present in
Avogadro 1. Both packages can be installed on the same system, and so it is
possible to try the latest without losing access to the previous version. We
will be making occasional releases of Avogadro 1.x too, along with migrating
functionality to Avogadro 2. We value your feedback, and hope that you will
find the improvements made in version 2 useful.

What does Avogadro 2 do?

  • We’ve tried to make the best, most intuitive “builder”
  • Interfaces to many common computational packages
  • Designed to help both educational users and advanced research
  • Plugins that allow it to be extended and customized
  • Can be extended with simple Python scripts for file IO and input
    generation
  • Well defined public API, libraries and modular design

Download: Avogadro - Browse /avogadro2/0.7.0 at SourceForge.net

What’s new? See the Release Notes:
Avogadro2 0.7.0 - wiki.openchemistry.org

For more information: Avogadro - wiki.openchemistry.org

If you use Avogadro or Avogadro 2, please check out the recently published
Avogadro paper, and consider citing it:
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform | Journal of Cheminformatics | Full Text

This is a community project and we couldn’t have made this release without
you. Many thanks to all the contributors to Avogadro including those of you
who submitted feedback, bug reports, and code. We acknowledge that the
development of Avogadro 2 has been funded by a US Army SBIR with the
Engineering Research Development Center under contract (W912HZ-12-C-0005) at
Kitware, Inc.

–
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don’t have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics
Pro!
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affects their revenue. With AppDynamics, you get 100% visibility into your
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4

Thank you for your note. I tried all of the force fields on cyclohexane
with no change in the structure.

Stephen P. Molnar, Ph.D. Life is a fuzzy
set
Foundation for Chemistry Stochastic and
multivariate
www.FoundationForChemistry.com
(614)312-7528 (c)
Skype: smolnar1

-----Original Message-----
From: Marcus D. Hanwell [mailto:marcus.hanwell@kitware.com]
Sent: Tuesday, December 03, 2013 10:49 AM
To: avogadro-discuss@lists.sourceforge.net
Cc: Avogadro-devel Devel
Subject: Re: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

On Tue, Dec 3, 2013 at 8:25 AM, Stephen P. Molnar s.molnar@sbcglobal.net
wrote:

I must say that, in my opinion, this release is premature. I
appreciate the comment ’ lacks features present in Avogadro 1’, but
the new version appears to be incapable of rendering benzene as a planar
molecule at this point.
Although the optimized geometry of cyclohexane approximates the less
stable boat conformer, the 1.0 version will generate the more stable
chair conformer on optimization.

I would disagree, and think that ‘release early, release often’ is a useful
mantra in closing the loop between development and use that is employed by
many open source projects (including Avogadro in the past, and now). We
worked hard to ensure you could install Avogadro 1 and 2 on the same
machine, removing any requirement to choose one or the other. Perhaps this
article will fill add some of the motivation you appear to be inquiring
about,

http://www.kitware.com/source/home/post/113

When you say ‘incapable of rendering’ is this referring to the forcefield
optimization as your second point about cyclohexane is? I am not sure I see
any reason why a planar benzene would not render, but could see the
forcefield defaults giving issues. They both use the same forcefields
underneath (the ones developed by the Open Babel project), and I can look
into modifying our defaults as I had noticed version 2 generally didn’t
optimize the structures as well.

Is it possible that I am missing something in the new, more convoluted
directory and subdirectory structure of the gui?

It is, but you would have to be more specific for me to hope to answer your
question. If you are just interested in using the Avogadro application I am
not sure why this would concern you. Thank you for your feedback, if you
find Avogadro 2 unsuitable then certainly continue using 1.1 for now - we
have an update planned for that shortly too.

Sincerely,

Marcus

-----Original Message-----
From: Marcus D. Hanwell [mailto:marcus.hanwell@kitware.com]
Sent: Monday, December 02, 2013 2:14 PM
To: Avogadro-devel Devel; avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

We are very proud to announce the availability of Avogadro 2 0.7.0.

Avogadro 2 is a free, open source, cross-platform molecular editor
designed for flexible use in computational chemistry, molecular
modeling, bioinformatics, materials science, and related areas.
Packages are available for Windows, Linux and Mac OS X. The source
code source is available under the 3-clause BSD license.

Avogadro 2 is a rewrite of Avogadro, and still lacks features present
in Avogadro 1. Both packages can be installed on the same system, and
so it is possible to try the latest without losing access to the
previous version. We will be making occasional releases of Avogadro
1.x too, along with migrating functionality to Avogadro 2. We value
your feedback, and hope that you will find the improvements made in
version 2 useful.

What does Avogadro 2 do?

  • We’ve tried to make the best, most intuitive “builder”
  • Interfaces to many common computational packages
  • Designed to help both educational users and advanced research
  • Plugins that allow it to be extended and customized
  • Can be extended with simple Python scripts for file IO and input
    generation
  • Well defined public API, libraries and modular design

Download:
Avogadro - Browse /avogadro2/0.7.0 at SourceForge.net

What’s new? See the Release Notes:
Avogadro2 0.7.0 - wiki.openchemistry.org

For more information: Avogadro - wiki.openchemistry.org

If you use Avogadro or Avogadro 2, please check out the recently
published Avogadro paper, and consider citing it:
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform | Journal of Cheminformatics | Full Text

This is a community project and we couldn’t have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. We
acknowledge that the development of Avogadro 2 has been funded by a US
Army SBIR with the Engineering Research Development Center under
contract (W912HZ-12-C-0005) at Kitware, Inc.

–
Rapidly troubleshoot problems before they affect your business. Most
IT organizations don’t have a clear picture of how application
performance affects their revenue. With AppDynamics, you get 100%
visibility into your Java,.NET, & PHP application. Start your 15-day
FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.c
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Avogadro-Discuss@lists.sourceforge.net
avogadro-discuss List Signup and Options

-------- Rapidly troubleshoot problems before they affect your
business. Most IT organizations don’t have a clear picture of how
application performance affects their revenue. With AppDynamics, you
get 100% visibility into your Java,.NET, & PHP application. Start your
15-day FREE TRIAL of AppDynamics Pro!
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–
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don’t have a clear picture of how application performance
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5

On Tue, Dec 3, 2013 at 11:14 AM, Stephen P. Molnar
s.molnar@sbcglobal.netwrote:

Thank you for your note. I tried all of the force fields on cyclohexane
with no change in the structure.

Bear in mind that the conformer resulting from a computational geometry
optimization depends heavily on the starting structure. If the starting
structure is closer to boat, the optimization will follow the gradients to
the stationary point on the PES that corresponds to the boat structure, and
if the starting point is closer to chair, you will get chair. Try moving
some of the atoms to roughly form the chair, and then apply the
optimization. Note that this will happen with Avogadro 1 (or any other
computational code) as well.

Hope this helps,
Dave

Stephen P. Molnar, Ph.D. Life is a fuzzy
set
Foundation for Chemistry Stochastic and
multivariate
www.FoundationForChemistry.com
(614)312-7528 (c)
Skype: smolnar1

-----Original Message-----
From: Marcus D. Hanwell [mailto:marcus.hanwell@kitware.com]
Sent: Tuesday, December 03, 2013 10:49 AM
To: avogadro-discuss@lists.sourceforge.net
Cc: Avogadro-devel Devel
Subject: Re: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

On Tue, Dec 3, 2013 at 8:25 AM, Stephen P. Molnar s.molnar@sbcglobal.net
wrote:

I must say that, in my opinion, this release is premature. I
appreciate the comment ’ lacks features present in Avogadro 1’, but
the new version appears to be incapable of rendering benzene as a planar
molecule at this point.
Although the optimized geometry of cyclohexane approximates the less
stable boat conformer, the 1.0 version will generate the more stable
chair conformer on optimization.

I would disagree, and think that ‘release early, release often’ is a useful
mantra in closing the loop between development and use that is employed by
many open source projects (including Avogadro in the past, and now). We
worked hard to ensure you could install Avogadro 1 and 2 on the same
machine, removing any requirement to choose one or the other. Perhaps this
article will fill add some of the motivation you appear to be inquiring
about,

http://www.kitware.com/source/home/post/113

When you say ‘incapable of rendering’ is this referring to the forcefield
optimization as your second point about cyclohexane is? I am not sure I see
any reason why a planar benzene would not render, but could see the
forcefield defaults giving issues. They both use the same forcefields
underneath (the ones developed by the Open Babel project), and I can look
into modifying our defaults as I had noticed version 2 generally didn’t
optimize the structures as well.

Is it possible that I am missing something in the new, more convoluted
directory and subdirectory structure of the gui?

It is, but you would have to be more specific for me to hope to answer your
question. If you are just interested in using the Avogadro application I am
not sure why this would concern you. Thank you for your feedback, if you
find Avogadro 2 unsuitable then certainly continue using 1.1 for now - we
have an update planned for that shortly too.

Sincerely,

Marcus

-----Original Message-----
From: Marcus D. Hanwell [mailto:marcus.hanwell@kitware.com]
Sent: Monday, December 02, 2013 2:14 PM
To: Avogadro-devel Devel; avogadro-discuss@lists.sourceforge.net
Subject: [Avogadro-Discuss] Avogadro 2 0.7.0 Released

We are very proud to announce the availability of Avogadro 2 0.7.0.

Avogadro 2 is a free, open source, cross-platform molecular editor
designed for flexible use in computational chemistry, molecular
modeling, bioinformatics, materials science, and related areas.
Packages are available for Windows, Linux and Mac OS X. The source
code source is available under the 3-clause BSD license.

Avogadro 2 is a rewrite of Avogadro, and still lacks features present
in Avogadro 1. Both packages can be installed on the same system, and
so it is possible to try the latest without losing access to the
previous version. We will be making occasional releases of Avogadro
1.x too, along with migrating functionality to Avogadro 2. We value
your feedback, and hope that you will find the improvements made in
version 2 useful.

What does Avogadro 2 do?

  • We’ve tried to make the best, most intuitive “builder”
  • Interfaces to many common computational packages
  • Designed to help both educational users and advanced research
  • Plugins that allow it to be extended and customized
  • Can be extended with simple Python scripts for file IO and input
    generation
  • Well defined public API, libraries and modular design

Download:
Avogadro - Browse /avogadro2/0.7.0 at SourceForge.net

What’s new? See the Release Notes:
Avogadro2 0.7.0 - wiki.openchemistry.org

For more information: Avogadro - wiki.openchemistry.org

If you use Avogadro or Avogadro 2, please check out the recently
published Avogadro paper, and consider citing it:
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform | Journal of Cheminformatics | Full Text

This is a community project and we couldn’t have made this release
without you. Many thanks to all the contributors to Avogadro including
those of you who submitted feedback, bug reports, and code. We
acknowledge that the development of Avogadro 2 has been funded by a US
Army SBIR with the Engineering Research Development Center under
contract (W912HZ-12-C-0005) at Kitware, Inc.

–
Rapidly troubleshoot problems before they affect your business. Most
IT organizations don’t have a clear picture of how application
performance affects their revenue. With AppDynamics, you get 100%
visibility into your Java,.NET, & PHP application. Start your 15-day
FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.c
lktrk _______________________________________________
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-------- Rapidly troubleshoot problems before they affect your
business. Most IT organizations don’t have a clear picture of how
application performance affects their revenue. With AppDynamics, you
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15-day FREE TRIAL of AppDynamics Pro!
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organizations don’t have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
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