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<p class="MsoNormal">Thank you! I’ll keep in mind the other email address.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Regards,<o:p></o:p></p>
<p class="MsoNormal">Divita<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Elaine Meng <meng@cgl.ucsf.edu><br>
<b>Date: </b>Saturday, January 9, 2021 at 11:26 AM<br>
<b>To: </b>Divita Mathur <dmathur4@gmu.edu><br>
<b>Cc: </b>Chimera Dev <chimera-dev@cgl.ucsf.edu><br>
<b>Subject: </b>Re: [chimera-dev] Building custom nucleotides<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Hi Divita,<br>
A few answers between your questions below.<br>
<br>
> On Jan 8, 2021, at 4:10 PM, Divita Mathur <dmathur4@gmu.edu> wrote:<br>
> <br>
> Hi Eric<br>
> <br>
> 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?<br>
<br>
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@cgl.ucsf.edu<br>
> <br>
> 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.<br>
<br>
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).<br>
<br>
> Thanks,<br>
> Divita<br>
> <br>
Best,<br>
Elaine<br>
----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
<br>
> From: Eric Pettersen <pett@cgl.ucsf.edu><br>
> Date: Friday, January 8, 2021 at 4:49 PM<br>
> To: Divita Mathur <dmathur4@gmu.edu><br>
> Cc: chimera-dev@cgl.ucsf.edu <chimera-dev@cgl.ucsf.edu><br>
> Subject: Re: [chimera-dev] Building custom nucleotides<br>
> <br>
> Hi Divita,<br>
> 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.<br>
> 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.<br>
> <br>
> --Eric<br>
> <br>
> Eric Pettersen<br>
> UCSF Computer Graphics Lab<br>
> <br>
> On Jan 8, 2021, at 11:41 AM, Divita Mathur <dmathur4@gmu.edu> wrote:<br>
> <br>
> Hello!<br>
> <br>
> 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.<br>
> <br>
> For example, I want to create a T that has an amino linker…<br>
> <br>
> Regards,<br>
> Divita<o:p></o:p></p>
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