Avogadro not displaying some cube files from Q-Chem

General Discussion
1

Hi,

I am using Avogadro to visualize molecular orbitals generated from Q-
Chem as cube files. For some reason some will open and others will
not. I am uploading two examples works.cube and doesnotwork.cube to http://rapidshare.com/files/400448250/cube.zip.html
. Both were created with the same settings, and I don’t see why the
latter won’t work. I am running Avogadro 1.0.0 Git revision 81fcdfb on
Mac OS 10.5.8.

Any ideas on why this could be?

Thanks,
Eric

2

not. I am uploading two examples works.cube and doesnotwork.cube to http://rapidshare.com/files/400448250/cube.zip.html

As a general rule, we recommend adding “GUI=2” to the $rem section of Q-Chem files. This will spit out a formatted checkpoint file (FChk) which can be used to generate the cubes and is much smaller. (Avogadro will read file.FChk.gz as well and transparently uncompress.)

In this case, it’s pretty obvious. Q-Chem wrote blank lines in the middle of the cube. The easy workaround for now is:

grep -v ‘^$’ doesnotwork.cube >new.cube

Hope that helps,
-Geoff

3

Geoff,

Thank you so much for the excellent response. I appreciate it.

Eric

On Jun 30, 2010, at 8:57 AM, Geoffrey Hutchison wrote:

not. I am uploading two examples works.cube and doesnotwork.cube to http://rapidshare.com/files/400448250/cube.zip.html

As a general rule, we recommend adding “GUI=2” to the $rem section
of Q-Chem files. This will spit out a formatted checkpoint file
(FChk) which can be used to generate the cubes and is much smaller.
(Avogadro will read file.FChk.gz as well and transparently
uncompress.)

In this case, it’s pretty obvious. Q-Chem wrote blank lines in the
middle of the cube. The easy workaround for now is:

grep -v ‘^$’ doesnotwork.cube >new.cube

Hope that helps,
-Geoff

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