<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Divita,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>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.</div><div class=""><br class=""></div><div class=""><div class="">--Eric</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On Jan 8, 2021, at 11:41 AM, Divita Mathur <<a href="mailto:dmathur4@gmu.edu" class="">dmathur4@gmu.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Hello!<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">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.<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">For example, I want to create a T that has an amino linker…<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class=""><o:p class=""> </o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Regards,<o:p class=""></o:p></span></div><div style="margin: 0in; font-size: 12pt; font-family: Calibri, sans-serif;" class=""><span style="font-size: 11pt;" class="">Divita<o:p class=""></o:p></span></div></div><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">_______________________________________________</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><span style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none; float: none; display: inline !important;" class="">Chimera-dev mailing list</span><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="mailto:Chimera-dev@cgl.ucsf.edu" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Chimera-dev@cgl.ucsf.edu</a><br style="caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;" class=""><a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev</a></div></blockquote></div><br class=""></div></body></html>