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<p class="MsoNormal">Hi Eric<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<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">Eric Pettersen <pett@cgl.ucsf.edu><br>
<b>Date: </b>Friday, January 8, 2021 at 4:49 PM<br>
<b>To: </b>Divita Mathur <dmathur4@gmu.edu><br>
<b>Cc: </b>chimera-dev@cgl.ucsf.edu <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">Hi Divita,<o:p></o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal">--Eric<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Eric Pettersen<o:p></o:p></p>
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<p class="MsoNormal">UCSF Computer Graphics Lab<o:p></o:p></p>
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<p class="MsoNormal">On Jan 8, 2021, at 11:41 AM, Divita Mathur <<a href="mailto:dmathur4@gmu.edu">dmathur4@gmu.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hello!<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">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.<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">For example, I want to create a T that has an amino linker…<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Regards,<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal">Divita<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:Helvetica">_______________________________________________<br>
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