Windows/Linux questions again


Sorry about that - I hit send instead of save by accident.

I have just joined the list and thought I should introduce myself. I teach chemistry at a small private college in Michigan and I would like to help with Avogadro. I don’t have much programming background, but I thought I would be able to help with the documentation. I am particularly interested in the Education examples on the wiki.

I have both Windows and Linux installed on my laptop, so I thought I would try Avogadro on both. I’m running:

Windows XP using Avogadro 0.9.7

Ubuntu (Jaunty) 9.04 using Avogadro 0.9.6.

I’m new to Ubuntu and a little unsure about compiling from source, so I am using the most recent version of Avogadro I could access from the Debichem repository as described on the Distribution Packages page of the wiki.

In playing around with Avogadro I noticed a number of discrepancies between the Linux version and the Windows version. Some of the Linux problems I’m seeing may have been fixed in 0.9.7, but I’ll include them in case this is incorrect.

  1. On both platforms I have seen the 3d molecule window fail to show the molecule - instead the desktop background "bleeds through"
    on Linux this goes away if I turn off all Visual Effects in the desktop settings
    on Windows I was running a program called Samurize ( If I turn Samurize off, the molecule displays correctly

  2. display dipoles in Linux - if I edit the molecule or start a new molecule after I have used the Display Dipole option, the program crashes. Even if I first turn off Dipoles.

This does not happen with Windows

 One other comment about the Dipole display in both Linux and Windows:  I found it difficult to see the dipole arrow, depending on the angle and lighting.  Maybe a different arrow style would work better   - like the arrows used when the axes are displayed.
  1. Using Conformer Search
    in Linux, Avogadro crashes
    in Windows I can see that something happens, but I can’t tell how to see the results.

  2. Insert fragment in the Build menu
    in Linux this opens the fragments folder - I think correctly
    in Windows this opens the c:/Program Files/Avogadro folder and you have to navigate down through several directories to get to
    c:/Program Files/Avogadro/share/avogadro/fragments once there, you can select and insert the fragment

  3. the Center option on the View menu does work in Linux, but not in Windows.

I hope this is useful. Thanks for your help,


Dr. Steven P. Wathen
Associate Professor of Chemistry
Siena Heights University
1247 East Siena Heights Drive
Adrian, MI 49221

(517) 264-7657