Thanks for your answer Geoff,

I don't think it's my video driver because when I install avogadro from 
the repository with apt-get, it works fine (except that avogadro crash 
when I want to save).

You're right, the problem don't come from libpng because I've got the 
same message when I run the fonctionnal avogadro 1.0.3 caught with 
apt-get.(libpng warning: Ignoring attempt to set cHRM RGB triangle with 
zero area)

The atoms are really created but not displayed(seen from the cartesian 
editor)

The display is checked.

I've also tried to use the avogadro-squared git but there's a problem 
cloning the openbabel git

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Cloning into 'openbabel'...
remote: Counting objects: 39465, done.
remote: Compressing objects: 100% (7170/7170), done.
remote: Total 39465 (delta 32101), reused 39412 (delta 32066)
Receiving objects: 100% (39465/39465), 30.23 MiB | 3.43 MiB/s, done.
Resolving deltas: 100% (32101/32101), done.
fatal: reference is not a tree: 2d41e95c6c94d8eab39ddc3459f990b47fcf2e51
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Remark: you may need to add the "make" line in the wiki page 
http://avogadro.openmolecules.net/wiki/Compiling_on_Linux_and_Mac_OS_X 
for beginners like me!

Thanks for your help.

Benjamin ABEL
Chemistry teacher in Nice(France)

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