[Chimera-users] Defining glycosidic bond of nucleotide objects

Charles-Alexandre Mattelaer charlesalexandre.mattelaer at kuleuven.be
Tue Apr 4 02:54:11 PDT 2017

Dear Chimera-users

I'm currently doing modeling on hexitol nucleic acids and using Chimera to visualize the trajectories. Since the atoms in the hexitol-ring are numbered differently than in the standard ribose, Chimera has some difficulties displaying the correct ribbon (backbone) and slab (bases). I've been able to define my own ribbon style using the Ribbon Style Editor and creating a new ribbon style based on the standard 'nuleic acid' trace and replacing the existing backbone atoms with the corresponding atom names for the non-standard hexitol residues.

The main problem is setting a slab object to replace the base atoms. The 'nucleotide objects' settings are based on a glycosidic bond on the C1' of ribose. In HNA the glycosidic bonds are found on C2' of hexitol. I believe this is causing the problem. Additionally, I can add that using the 'ladder'-like objects, a gap between the 'steps' and the backbone occurs. (I've tried setting the base as anchor but to no avail.) I was wondering if there would be a way to redefine the anchor atom of the nucleotide objects? (I searched in the manual but haven't found any ways to redefine the anchor itself.) This would greatly improve visibility of larger oligonucleotides and would help me a lot.

Kind regards and thank you in advance

Charles-Alexandre Mattelaer
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