SUBSTITUTE atom by fragment

General Discussion
1

Dear all,

I would like to substitute an atom by a fragment
using Avogadro (version 0.9.8 / MacOs). However, using the “insert” menu
in Avogadro does not SUBSTITUTE the selected atom,
but INSERT the selected fragment into the windows instead.

Is there any possibility to do that in Avogadro ? That would
be easier to build a large chemical system
by simply growing a small starting atoms set.

Thanks in advance.
Eric H.

2

Is there any possibility to do that in Avogadro ? That would
be easier to build a large chemical system
by simply growing a small starting atoms set.

It’s something I’m working on… Suggestions for how you’d like to see the interface would be welcome. I’m thinking it would be a new tool.

-Geoff

3

Dear Geoff,

Thanks for your answer.

We are currently developping
the Wiimote extension (Michael Gadroy
has been working on that for 8 months in our lab., and most
of the manipulation, rotation, selection, construction, measure tools
have been coded that will be made available
in a few weeks for Avogadro users) that
employs the Avogadro possibilities.
We would like also to implement this building possibility.

Concerning the interface that could be envisaged :

  1. after selecting an atom

  2. select a “SUBSTITUTE atom by fragment” menu
    (as for INSERT using the “Building” menu)

  3. choose a fragment in the library

  4. the selected atom will be substituted by this fragment

I think that should be very similar to the INSERT menu.

As an example, Molden proposes
such a possibility that is very easy to use.

In my opinion, the “fragment” word (french version of Avogadro)
is not exactly appropriate
in the current INSERT menu because
this possibility inserts a FULL molecule while
the SUBSTITUTE menu would
use a fragment, i.e a molecule with
the “link atom” removed.

Once more, thanks for developping Avogadro which
is a very helpful tools both in research and education !

Eric H.

Le 16 sept. 2010 à 17:16, Geoffrey Hutchison a écrit :

Is there any possibility to do that in Avogadro ? That would
be easier to build a large chemical system
by simply growing a small starting atoms set.

It’s something I’m working on… Suggestions for how you’d like to see the interface would be welcome. I’m thinking it would be a new tool.

-Geoff

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4

We are currently developing the Wiimote extension (Michael Gadroy has been working on that for 8 months in our lab., and most of the manipulation, rotation, selection, construction, measure tools

Cool! I’m glad to know that code is being updated. It seemed like a great idea, so I’m looking forward to seeing the possibility.

  1. select a “SUBSTITUTE atom by fragment” menu
    (as for INSERT using the “Building” menu)

This part is tricky. At the moment, there is no signal that the user selected anything. So right now, we can’t change the menu item.

  1. choose a fragment in the library
  2. the selected atom will be substituted by this fragment

I’ve been imagining an interface with a tool – the user clicks on an atom, which is immediately replaced by the fragment. For the tool, the user could also select a particular atom in the fragment for bonding (e.g., axial vs. equatorial positions in a cyclohexane). GaussView and Spartan function along these lines.

But I did take some time today and code an improvement to the insert fragment and SMILES commands which functions the way you describe. It’s not as flexible, since it automatically picks the first atom in the fragment for bonding. But it works and will serve as the start of the tool.

If you use a Mac, it will become part of the nightly unstable builds. Otherwise it will probably take a few days before it becomes part of the “master” development code.

In my opinion, the “fragment” word (french version of Avogadro)
is not exactly appropriate

I haven’t looked at the French translation. In English, we’re trying to use the sense of “a small piece” for fragment (i.e., it may be an isolated molecule, but it’s intended to become a small piece of the whole).

Certainly we’re open to patches, either to the insert commands or to the translations!

Once more, thanks for developping Avogadro which
is a very helpful tools both in research and education !

Our pleasure!

Best regards,
-Geoff

5

Dear Geoff.

Thank you for your proposition.
We downloaded the latest nightly unstable build (1.1.0) for Mac,
but have not found this new possibility.
Is the new improvement coded to the insert fragment menu ?
Thanks in advance.
Sincerely.
Eric

Le 17 sept. 2010 à 20:51, Geoffrey Hutchison a écrit :

We are currently developing the Wiimote extension (Michael Gadroy has been working on that for 8 months in our lab., and most of the manipulation, rotation, selection, construction, measure tools

Cool! I’m glad to know that code is being updated. It seemed like a great idea, so I’m looking forward to seeing the possibility.

  1. select a “SUBSTITUTE atom by fragment” menu
    (as for INSERT using the “Building” menu)

This part is tricky. At the moment, there is no signal that the user selected anything. So right now, we can’t change the menu item.

  1. choose a fragment in the library
  2. the selected atom will be substituted by this fragment

I’ve been imagining an interface with a tool – the user clicks on an atom, which is immediately replaced by the fragment. For the tool, the user could also select a particular atom in the fragment for bonding (e.g., axial vs. equatorial positions in a cyclohexane). GaussView and Spartan function along these lines.

But I did take some time today and code an improvement to the insert fragment and SMILES commands which functions the way you describe. It’s not as flexible, since it automatically picks the first atom in the fragment for bonding. But it works and will serve as the start of the tool.

If you use a Mac, it will become part of the nightly unstable builds. Otherwise it will probably take a few days before it becomes part of the “master” development code.

In my opinion, the “fragment” word (french version of Avogadro)
is not exactly appropriate

I haven’t looked at the French translation. In English, we’re trying to use the sense of “a small piece” for fragment (i.e., it may be an isolated molecule, but it’s intended to become a small piece of the whole).

Certainly we’re open to patches, either to the insert commands or to the translations!

Once more, thanks for developping Avogadro which
is a very helpful tools both in research and education !

Our pleasure!

Best regards,
-Geoff

Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev

Avogadro-Discuss mailing list
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avogadro-discuss List Signup and Options

Eric Henon
Professeur
Universite de Reims Champagne-Ardenne
Institut de Chimie Moleculaire de Reims
http://www.univ-reims.fr/ICMR
CNRS UMR 6229
UFR des Sciences Exactes et Naturelles
BP 1039
51687 Reims Cedex 2 (France)
Tél./Fax : + 33 (0) 3 26 91 84 97
eric.henon@univ-reims.fr

6

Hi,
Can you tell me how to start the orbital engine in Avogadro? I have
drawn a benzene ring and optimized the geometry. I now want to view the
orbitals, but the tool settings does not seem to have an orbital
options. I did see orbitals being generated from the tool settings menu
in the demo of (an earlier?) Avogadro on Showmedo.com. Is the orbital
engine still present?

Thanks,
Tim