Problem with a cube file

Dear all,
I am trying to plot an electron density starting from a cube file, whose
header is reported below:
cube file
generated by DIRAC
3 -10.000000 -10.000000 -15.701543
80 0.253165 0.000000 0.000000
80 0.000000 0.253165 0.000000
80 0.000000 0.000000 0.397507
53 53.000000 0.000000 0.000000 0.000000
53 53.000000 0.000000 0.000000 5.701543
53 53.000000 0.000000 0.000000 -5.701543

To generate the plot, I loaded the file then went to Extensions ->
Create Surfaces and select cube files in both dropdown menus.

The problem I encounter is that the plotted density is shifted from the
atoms, without any particular reason apparently. I attached a png of the
Avogadro rendering and the ParaView rendering, so that you can see more
clearly what I mean.
Best regards.


Roberto Di Remigio

Hi Roberto,

I had what looks like a similar problem to yours about a year or so
ago with .cube files for molecular orbitals generated from Q-Chem. We
posted a bug report
(http://sourceforge.net/tracker/?func=detail&aid=3132575&group_id=165310&atid=835077),
and it appears that they made a patch in response to the issue. I have
not used Avogadro for a while but thought this may be useful to know.

Best,
Eric Isaacs

On Tue, Jun 5, 2012 at 12:09 PM, Roberto Di Remigio
roberto.diremigio@gmail.com wrote:

Dear all,
I am trying to plot an electron density starting from a cube file, whose
header is reported below:
cube file
generated by DIRAC
3 -10.000000 -10.000000 -15.701543
80 0.253165 0.000000 0.000000
80 0.000000 0.253165 0.000000
80 0.000000 0.000000 0.397507
53 53.000000 0.000000 0.000000 0.000000
53 53.000000 0.000000 0.000000 5.701543
53 53.000000 0.000000 0.000000 -5.701543

To generate the plot, I loaded the file then went to Extensions -> Create
Surfaces and select cube files in both dropdown menus.

The problem I encounter is that the plotted density is shifted from the
atoms, without any particular reason apparently. I attached a png of the
Avogadro rendering and the ParaView rendering, so that you can see more
clearly what I mean.
Best regards.


Roberto Di Remigio


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The problem I encounter is that the plotted density is shifted from the atoms, without any particular reason apparently. I attached a png of the Avogadro rendering and the ParaView rendering, so that you can see more clearly what I mean.

At the moment, the Open Babel cube code (used by Avogadro) assumes that the step size is the same in the x, y, and z directions, which is not true in your cube file.

It’s a known bug, as mentioned earlier. The patch solves some of the problem but not the core issue.

This part of the code is under rewrite, so we hope to have a better fix soon.

Thanks,
-Geoff

On 06/05/2012 09:39 PM, Geoff Hutchison wrote:

The problem I encounter is that the plotted density is shifted from the atoms, without any particular reason apparently. I attached a png of the Avogadro rendering and the ParaView rendering, so that you can see more clearly what I mean.
At the moment, the Open Babel cube code (used by Avogadro) assumes that the step size is the same in the x, y, and z directions, which is not true in your cube file.

It’s a known bug, as mentioned earlier. The patch solves some of the problem but not the core issue.

This part of the code is under rewrite, so we hope to have a better fix soon.

Thanks,
-Geoff
Ok, I understand. Thanks a lot!


Roberto Di Remigio

At the moment, there is no patch. This would require a sizable change to the Open Babel library which Avogadro uses.

My suggestion would be to try VMD for now.

Sorry I can’t be of more help,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

On Feb 9, 2013, at 10:25 PM, Eduard Matito ematito@gmail.com wrote:

Dear Geoff,

I’m an Avogadro user that has encountered the same problem with cube files.
As other users noticed the plot is shifted and I already noticed that the problem
is that Avogadro is not reading stepsize for x,y,z separately. I have just seen
a mailing list reporting this problem on June. I downloaded the last Mac version
and the bug is still there. Did you get a patch/version that deals with this problem?

Thanks in advance,

Eduard


Eduard Matito
Institut de Química Computacional
University of Girona
17071 Girona (Catalonia) Spain
Phone: +34972419541
http://ematito.webs.com

Ok, I see. Thanks.
Eduard

On Feb 12, 2013, at 3:36 AM, Geoffrey Hutchison geoff.hutchison@gmail.com wrote:

At the moment, there is no patch. This would require a sizable change to the Open Babel library which Avogadro uses.

My suggestion would be to try VMD for now.

Sorry I can’t be of more help,
-Geoff


Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoff.hutchison@gmail.com
web: http://hutchison.chem.pitt.edu/

On Feb 9, 2013, at 10:25 PM, Eduard Matito ematito@gmail.com wrote:

Dear Geoff,

I’m an Avogadro user that has encountered the same problem with cube files.
As other users noticed the plot is shifted and I already noticed that the problem
is that Avogadro is not reading stepsize for x,y,z separately. I have just seen
a mailing list reporting this problem on June. I downloaded the last Mac version
and the bug is still there. Did you get a patch/version that deals with this problem?

Thanks in advance,

Eduard


Eduard Matito
Institut de Química Computacional
University of Girona
17071 Girona (Catalonia) Spain
Phone: +34972419541
http://ematito.webs.com


Eduard Matito
Institut de Química Computacional
University of Girona
17071 Girona (Catalonia) Spain
Phone: +34972419541
http://ematito.webs.com