[chimera-dev] Building custom nucleotides

[Elaine Meng]

Hi Divita,
A few answers between your questions below.

> On Jan 8, 2021, at 4:10 PM, Divita Mathur <dmathur4 at gmu.edu> wrote:
> 
> 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?

That is the only way, if you are using Chimera.  Eric was suggesting a way to do exactly the same Chimera functions with code instead, since you asked on the programming mailing list (chimera-dev), but the method is the same.  For future reference, if you just want to ask non-programming questions about Chimera, the better e-mail address is chimera-users at cgl.ucsf.edu
>  
> 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.

No, we have not been planning to add other nucleotides, especially not any with different backbones like PNA (peptide nucleic acids) and LNA (locked nucleic acids).

> Thanks,
> Divita
>  
Best,
Elaine
----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> 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> 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