[chimera-dev] Building custom nucleotides

[Eric Pettersen]

Hi Divita,
	While theoretically possible via some precise and difficult tinkering with data files in BuildStructure as well as it's placeNucleotide() routine, I wouldn't recommend that approach -- it's just too hard and too much work.
	What I would recommend instead is to add your modified Ts as regular Ts and afterward select the atoms where the modification occurs and use a custom Python script to make the modification.  The script would loop through chimera.selection.currentAtoms() and use chimera.molEdit.addDihedralAtom(new_atom_name, element, from_atom, dihed2_atom, dihed3_atom, bond_dist, angle, dihedral, bonded=True) to add the modification atom by atom.  Let me know if you need more guidance than this.

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jan 8, 2021, at 11:41 AM, Divita Mathur <dmathur4 at gmu.edu> wrote:
> 
> Hello!
>  
> I am using the Build structure to create DNA duplexes with ATGC bases. However, I want to insert Ts that are slightly modified. I can go in and modify each T but I was wondering if I can make a modified-T “template” , assign it a new letter (say X) and then use it in the Build structure function. The backbone and base pairing rules of the new T would be the same.
>  
> For example, I want to create a T that has an amino linker…
>  
> Regards,
> Divita
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