I am a chemistry student and a fan of avogadro. Thank you for creating this very useful software.
For the last 2 months or so, avogadro 1.2 has suddenly stopped recognizing atoms. As an example, I have attached a figure of a molecule (S-BINAP) that I loaded and tried to select all the atoms using the selection tool. In this case, atoms should also be highlighted in light blue, but as you can see, only bonds are highlighted in light blue. It seems that the atoms are not recognized. I have examined various file formats, but have not been able to improve the situation.
I am using avogadro 1.2 in windows 11 environment. Similarly, my friend who is using avogadro1.2 on windows 11 seems to be working fine. So it is probably not a bug but my personal problem.
What could be the cause in this case? Any advice would be appreciated.
Operating system and version:Windows 11 Home 22H2
@yoshito Note, Avogadro 1.2 no longer is under active development and maintenance. Instead, consider to use the current branch leading to Avogadro 2.0. The GitHub repository offers binaries for Linux, MacOS, and Windows; they are updated regularly.
In the case of the Linux AppImage (version 1.97, just downloaded again), picking the chemical name from the English edition of Wikipedia, 2,2′-bis(diphenylphosphino)-1,1′-binaphthyl, File → Import → Download by Name offered rapid access to the one of the two enantiomers. Then, Select → Select by Element (where I selected carbon)
worked just fine, as did e.g., the selection of all atoms (Select → Select All, or the short cut key combination Ctrl + A):
where the corresponding atoms got their highlighting mark. Check if your platform and installation of newer Avogadro equally offers this function.
I suspect this might just be a rendering issue. If you cut / copy the selected atoms, are they copied / modified?
As @Thomas indicated, we cannot maintain Avogadro 1.2 anymore, but if the bonds are selected, the atoms should be. On the other hand, that doesn’t mean your graphics driver on Windows likes rendering the transparent blue spheres…
So I suspect the issue may be with rendering the selected spheres in Avo 1.2, not that the atoms are unrecognized.
Thank you, I will try to get back to you.Sorry for the late reply.
The problem was resolved yesterday. As @ghutchis said, it seems to be a graphics problem.I am using Ryzen 7 5825U (AMD Radeon Graphics) and the problem was improved by re-installing the graphics driver.
Avogadro2 is working fine. I am looking forward to even more functionality.
Thank you very much for your help and advice!
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