[chimera-dev] Building custom nucleotides

[Divita Mathur]

Hi Eric

I see, not a problem. Instead of script I have used the Modify structure and change one hydrogen at a time to add the next atom by selecting the correct number of bonds and shape (linear/trigonal/tetrahedral). Is that another acceptable way of doing it?

Have you considered adding other nucleic acids in the alphabet available in Chimera? Such as PNA or LNA? I have built them from scratch and then used “Minimize Structure” for achieving the reasonable bond angle/lengths.

Thanks,
Divita

From: Eric Pettersen <pett at cgl.ucsf.edu>
Date: Friday, January 8, 2021 at 4:49 PM
To: Divita Mathur <dmathur4 at gmu.edu>
Cc: chimera-dev at cgl.ucsf.edu <chimera-dev at cgl.ucsf.edu>
Subject: Re: [chimera-dev] Building custom nucleotides
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<mailto: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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