Highlight issues in selection tool

General Discussion Support
1

Hi there!

First of all many thanks in advance and for the amazing job developing Avogadro. I love it!!! However, I believe this to be a bug with Avogadro

Environment Information

Avogadro version: 1.100.0
Operating system and version: Windows 10 Enterprise LTSC

When using the selection tool and selecting the desired atoms they are not highlighted. Once selected although I cannot see that they are selected I can do with the atoms whatever I want as if they were selected. Nonetheless, they are not highlighted in the characteristic blue.

In summary the selection tool works fine but I am not able to see which atoms are selected.

In this image the whole molecule is selected:

image
image1919Ă—1141 88.6 KB

2

Hmm. If you click on the ball-and-stick display type, it should bring up some configuration options in the panel.

If you change the opacity of the balls-and-sticks, do you see them?

In other words, is this a problem specifically with selection or with displaying translucent rendering on your system?

3

There’s an issue on GitHub for this, by the way.

For me at least, no. In fact doing this led me to stumble on another bug – if I reduce the opacity at all, the balls immediately vanish (the sticks on the other hand scale smoothly in translucency).

@brockdyer03 also said he has the same issue on his Windows system, I can’t remember if he’s on Win 10 or 11.

4

Sorry, I didn’t see the GitHub issue. By doing what you mentioned @ghutchis nothing changes :frowning: I’m unable to see the highlight.

5

No, my comment wasn’t about the highlight - it was about the atoms.

6

Weird. On my Mac, I obviously have no such issue.

Try git revert d8785f5 to see if that commit (and the culling) is the issue.

If so, I guess I can only enable culling on Mac? So much for cross-platform rendering with OpenGL.

7

Unfortunately I can’t compile locally at the moment as the linking stage fails:

...
[100%] Linking CXX executable ../bin/avogadro2
/usr/lib64/gcc/x86_64-suse-linux/14/../../../../x86_64-suse-linux/bin/ld: /home/matt/avo/qt6/prefix/lib64/libAvogadroRendering.so.1.100.0: undefined reference to `__glewCompileShader@G_'
/usr/lib64/gcc/x86_64-suse-linux/14/../../../../x86_64-suse-linux/bin/ld: /home/matt/avo/qt6/prefix/lib64/libAvogadroRendering.so.1.100.0: undefined reference to `__glewGenBuffers@G_'
...
/usr/lib64/gcc/x86_64-suse-linux/14/../../../../x86_64-suse-linux/bin/ld: /home/matt/avo/qt6/prefix/lib64/libAvogadroRendering.so.1.100.0: undefined reference to `__glewCreateShader@G_'
collect2: error: ld returned 1 exit status
gmake[5]: *** [avogadro/CMakeFiles/avogadro.dir/build.make:301: bin/avogadro2] Error 1
...

Any idea what’s going on there? I have glew-devel and libGLEW2_2 installed, which always used to be enough afaik, but not glew or libGLEW_EGL2_2.

8

It’s building fine via GitHub - I would rebuild from scratch?

9

That was despite rebuilding from scratch :slight_smile: I just wondered if you knew of a change from recent months that might have caused the glew stuff to stop working on my system

10

Not offhand, no. We haven’t changed anything involving glew yet.

1 Like
11

@ghutchis Sorry for the misunderstanding. If I change the opacity the “balls” disappear. I think this is the other bug @matterhorn103 commented.

image
image1919Ă—1158 128 KB

12

@Marti_Sidro I’m able to replicate your observation of a ball-stick model to change into a stick-only one with the current nightly build for Windows (commit 1.100.0-27-gf3131df) in an environment of Windows 10/64bit:

2025-06-03_screencast

which wasn’t present with the release version of 1.100 installed earlier. With the nightly built installed on top of the release, I equally observed a selection of a few atoms by dragging the rectangle / mouse tapping on individual atoms or of the whole molecule (Ctrl + A) no longer yielded the blue halos.

1 Like
13

Yep. Should be fixed in the next nightly release.

14

Nice! Thank you very much! I’ll wait then!