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@cgl.ucsf.edu>
Date: Friday, January 8, 2021 at 4:49 PM
To: Divita Mathur <dmathur4@gmu.edu>
Cc: chimera-dev@cgl.ucsf.edu <chimera-dev@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