On 16/03/2025 18:18, Marco Bravo wrote:
Hello All
Hello Marco.
I managed to place some DNA bases in my map using the build DNA/RNA model feature in coot after putting in my sequence. I see density for one more base I can model in. How do I add one more base to the 5' position of my DNA? when I click add residue on the vertical toolbar the new nucleotide gets added but connected to the existing DNA chain very incorrectly as in the DNA bases are connected to each other and not the 5' and 3' connectivity I am looking for.
Hmm. this sounds like a bug. Which version of Coot are you using? Did you get it from CCP4?
That is the tool that I intended you to use. Coot uses LSQ superposition of an ideal B-form helix to determine the positions of the next residue (the map is not used). Maybe things are getting messed up because your current residue is not like a B-form helix. Maybe the residue numbers are not arranged in a way that Coot expects.
If you like you can send me the coordinates of the chain, in confidence, and I will have a look.
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