How do I access the Z-matrix tool?

I’m interested in using the Z-matrix
toolhttp://avogadro.cc/wiki/Z-Matrix_Toolin Avogadro. I’m currently
using Avogadro v1.1.1, and the tool does not
appear in the toolbar or the menus. Can I enable it, or do I need to
download a newer build to get it?

Thanks in advance,

Rick


Rick Muller
rpmuller@gmail.com
505-750-7557

Hi Rick,

On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmuller@gmail.com wrote:

I’m interested in using the Z-matrix tool in Avogadro. I’m currently using
Avogadro v1.1.1, and the tool does not appear in the toolbar or the menus.
Can I enable it, or do I need to download a newer build to get it?

It is not enabled by default because I never got it working in a
robust way. It is enabled by a build flag, I could enable it in the
next release builds by default (and would like to revisit this as it
would be great to get working).

Thanks,

Marcus

Marcus,

Thanks for the reply. What’s the probably getting the zmatrix robust? Is it
the conversion to cartesian coordinates, or the interaction with the rest
of Avogadro? I might be able to help with the former, but probably not the
latter.

Rick

On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell <
marcus.hanwell@kitware.com> wrote:

Hi Rick,

On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmuller@gmail.com wrote:

I’m interested in using the Z-matrix tool in Avogadro. I’m currently
using
Avogadro v1.1.1, and the tool does not appear in the toolbar or the
menus.
Can I enable it, or do I need to download a newer build to get it?

It is not enabled by default because I never got it working in a
robust way. It is enabled by a build flag, I could enable it in the
next release builds by default (and would like to revisit this as it
would be great to get working).

Thanks,

Marcus


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Rick Muller
rpmuller@gmail.com
505-750-7557

Rick,

It is the former (to/from Cartesian, corner cases), it was also in
progress as I moved between positions and I never got around to it. I
would welcome input on robust implementations, and can handle the
Avogadro side. I would gladly update the Avogadro 1.1 version, and am
eager to port this to Avogadro 2.

Thanks,

Marcus

On Mon, Apr 7, 2014 at 4:36 PM, Rick Muller rpmuller@gmail.com wrote:

Marcus,

Thanks for the reply. What’s the probably getting the zmatrix robust? Is it
the conversion to cartesian coordinates, or the interaction with the rest of
Avogadro? I might be able to help with the former, but probably not the
latter.

Rick

On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

Hi Rick,

On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmuller@gmail.com wrote:

I’m interested in using the Z-matrix tool in Avogadro. I’m currently
using
Avogadro v1.1.1, and the tool does not appear in the toolbar or the
menus.
Can I enable it, or do I need to download a newer build to get it?

It is not enabled by default because I never got it working in a
robust way. It is enabled by a build flag, I could enable it in the
next release builds by default (and would like to revisit this as it
would be great to get working).

Thanks,

Marcus


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Rick Muller
rpmuller@gmail.com
505-750-7557


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I have some python code that I’ll start to stress test and maybe commit to
the PyQuante2 repository sometime real soon. There’s probably nothing
valuable in the code right now, but maybe after the debugging process I’ll
know enough to help out with the process.

Guess I should figure out how to build Avogadro…

On Mon, Apr 7, 2014 at 2:45 PM, Marcus D. Hanwell <
marcus.hanwell@kitware.com> wrote:

Rick,

It is the former (to/from Cartesian, corner cases), it was also in
progress as I moved between positions and I never got around to it. I
would welcome input on robust implementations, and can handle the
Avogadro side. I would gladly update the Avogadro 1.1 version, and am
eager to port this to Avogadro 2.

Thanks,

Marcus

On Mon, Apr 7, 2014 at 4:36 PM, Rick Muller rpmuller@gmail.com wrote:

Marcus,

Thanks for the reply. What’s the probably getting the zmatrix robust? Is
it
the conversion to cartesian coordinates, or the interaction with the
rest of
Avogadro? I might be able to help with the former, but probably not the
latter.

Rick

On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

Hi Rick,

On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmuller@gmail.com
wrote:

I’m interested in using the Z-matrix tool in Avogadro. I’m currently
using
Avogadro v1.1.1, and the tool does not appear in the toolbar or the
menus.
Can I enable it, or do I need to download a newer build to get it?

It is not enabled by default because I never got it working in a
robust way. It is enabled by a build flag, I could enable it in the
next release builds by default (and would like to revisit this as it
would be great to get working).

Thanks,

Marcus


Put Bad Developers to Shame
Dominate Development with Jenkins Continuous Integration
Continuously Automate Build, Test & Deployment
Start a new project now. Try Jenkins in the cloud.
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Rick Muller
rpmuller@gmail.com
505-750-7557


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Rick Muller
rpmuller@gmail.com
505-750-7557

Hi,

If you’re working on code to create z-matricies, then there is code in the
CCP1GUI that might be of interest to you. You can find the CCP1GUI here:

The main code to generate the zmatrix is the autoz routine here:

http://ccp1gui.cvs.sourceforge.net/viewvc/ccp1gui/ccp1gui/objects/zmatrix.py?view=markup

I know that Paul Sherwood (who wrote it) sent a lot of time sorting out
various corner cases and it’s pretty robust for even quite large molecules.

Hopefully this will give you some useful pointers and potentially working
code if you’re developing something similar yourself.

I’m sure that a zmatrix utility that could be used and shared by a variety
of codes would be a really welcome addition to the community.

Best wishes,

Jens

On 7 April 2014 21:47, Rick Muller rpmuller@gmail.com wrote:

I have some python code that I’ll start to stress test and maybe commit to
the PyQuante2 repository sometime real soon. There’s probably nothing
valuable in the code right now, but maybe after the debugging process I’ll
know enough to help out with the process.

Guess I should figure out how to build Avogadro…

On Mon, Apr 7, 2014 at 2:45 PM, Marcus D. Hanwell <
marcus.hanwell@kitware.com> wrote:

Rick,

It is the former (to/from Cartesian, corner cases), it was also in
progress as I moved between positions and I never got around to it. I
would welcome input on robust implementations, and can handle the
Avogadro side. I would gladly update the Avogadro 1.1 version, and am
eager to port this to Avogadro 2.

Thanks,

Marcus

On Mon, Apr 7, 2014 at 4:36 PM, Rick Muller rpmuller@gmail.com wrote:

Marcus,

Thanks for the reply. What’s the probably getting the zmatrix robust?
Is it
the conversion to cartesian coordinates, or the interaction with the
rest of
Avogadro? I might be able to help with the former, but probably not the
latter.

Rick

On Mon, Apr 7, 2014 at 10:51 AM, Marcus D. Hanwell
marcus.hanwell@kitware.com wrote:

Hi Rick,

On Mon, Apr 7, 2014 at 12:46 PM, Rick Muller rpmuller@gmail.com
wrote:

I’m interested in using the Z-matrix tool in Avogadro. I’m currently
using
Avogadro v1.1.1, and the tool does not appear in the toolbar or the
menus.
Can I enable it, or do I need to download a newer build to get it?

It is not enabled by default because I never got it working in a
robust way. It is enabled by a build flag, I could enable it in the
next release builds by default (and would like to revisit this as it
would be great to get working).

Thanks,

Marcus


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Rick Muller
rpmuller@gmail.com
505-750-7557


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rpmuller@gmail.com
505-750-7557


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