Hi, I tried to build A-form and Z-form DNA helices with Avogadro’s “Build” tool. It appears that the helices are still B-form, and only the bp per turns is changed to 11, or 12. I think this should be an error.
I also found this old discussion: [Avogadro-Discuss] Right-Handed Z-DNA?
I don’t know what version you’re using, but Avogadro has relied on Open Babel’s DNA coordinate generation.
I’d be happy to add this to the list for Avogadro 2.0 release checklist, but I am not a biochemist and I don’t know where to get A-form or Z-form coordinates, nor do I have a good way to test that the generation was performed correctly.
If you have some suggestions, they would be most welcome.
Hi! Thanks a lot for your response!
The version I’m using is:
Application Version: 1.2.0 (Git revision: c1fcc5b)
Library Version: 1.2.0 (Git revision: c1fcc5b)
Open Babel Version: 2.3.90
Qt Version: 4.8.7
And I’m using an M1 macbook pro.
As for the DNA coordinates, probably you can collaborate with the developer of x3dna-dssr: https://x3dna.org/
As for now, my suggestion is to completely remove the A-form/Z-form options because they are very misleading.