Creating surface

Dear all,

I’m new to Avogadro and I’m particularly interested in its creating surface
feature, and I would like to perform the following task which I don’t know if
its possible to do in Avogado. I have a cube file which gives the the value
of a property in every point in space (within a defined grid). From that file
I can create a surface, but the problem comes when colouring that surface. I
want to colour it according to the values of a second property, stored in a
second cube file (with the same grid size and the same spacing between
points). However, I cannot figure out how to do this. Is it possible to get
what I want with Avogadro?

To put this in a more chemical context, what I want is to colour the Electron
Localisation Function (stored in cube1) according to the synnapticity of the
basins (stored in cube2). Synnapticity has very simple values, usually 0, 1
or 2.

Thanks for your help.

Cheers

Jose

want to colour it according to the values of a second property, stored in a
second cube file (with the same grid size and the same spacing between
points). However, I cannot figure out how to do this. Is it possible to get
what I want with Avogadro?

No, unfortunately, it is not yet possible to create a surface from one cube, but color based on another cube. We were just discussing this about a week ago, so it’s definitely on the “to do soon” list.

My hope is that we can start the 1.1.x development releases in October.

Sorry I can’t be more help,
-Geoff

Ok, I will be waiting for that version then. Thanks for your work.

Cheers,

Jose

On Sat 11 September 2010 19:52:14 Geoffrey Hutchison wrote:

want to colour it according to the values of a second property, stored in
a second cube file (with the same grid size and the same spacing between
points). However, I cannot figure out how to do this. Is it possible to
get what I want with Avogadro?

No, unfortunately, it is not yet possible to create a surface from one
cube, but color based on another cube. We were just discussing this about a
week ago, so it’s definitely on the “to do soon” list.

My hope is that we can start the 1.1.x development releases in October.

Sorry I can’t be more help,
-Geoff


José Antonio Gámez Martinez

Departamento de Química, C-IX
Universidad Autónoma de Madrid
Cantoblanco. 28049 Madrid. Spain
Tlf: 34-91-497 38 56
FAX: 34-91-497 52 38

In the meantime, Jmol may be able to do this.

Have a look at

Best regards, Jan

On Sep 13, 2010, at 10:39 AM, Jose Antonio Gamez Martinez wrote:

Ok, I will be waiting for that version then. Thanks for your work.

Cheers,

Jose

On Sat 11 September 2010 19:52:14 Geoffrey Hutchison wrote:

want to colour it according to the values of a second property, stored in
a second cube file (with the same grid size and the same spacing between
points). However, I cannot figure out how to do this. Is it possible to
get what I want with Avogadro?

No, unfortunately, it is not yet possible to create a surface from one
cube, but color based on another cube. We were just discussing this about a
week ago, so it’s definitely on the “to do soon” list.

My hope is that we can start the 1.1.x development releases in October.

Sorry I can’t be more help,
-Geoff


José Antonio Gámez Martinez

Departamento de Química, C-IX
Universidad Autónoma de Madrid
Cantoblanco. 28049 Madrid. Spain
Tlf: 34-91-497 38 56
FAX: 34-91-497 52 38


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Thanks for the tip. I will have a look at it.

Cheers,

Jose

On Monday 13 September 2010 13:38:43 you wrote:

In the meantime, Jmol may be able to do this.

Have a look at
http://molecularmodelingbasics.blogspot.com/2009/12/electrostatic-potential
-maps-reloaded.html

Best regards, Jan

On Sep 13, 2010, at 10:39 AM, Jose Antonio Gamez Martinez wrote:

Ok, I will be waiting for that version then. Thanks for your work.

Cheers,

Jose