<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 Yaikhomba,<div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Tristan’s answer is the only way to go in ChimeraX right now. Adding bonds via a tool or command is among the missing features we just haven’t gotten to yet. Alternatively, you could open your structure in Chiimera, make the the bond, and write out a PDB you could then open in ChimeraX.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>If you are going to be adding more than one bond, you can make Tristan’s method a little easier to access by turning the Python code into a “preset”. You would save his code into a file, and then follow the instructions in Presets→Add A Preset… to turn it into a preset (probably named something like “New Bond”). To use it you would then select two atoms and choose the New Bond preset.</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><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 7, 2020, at 8:30 AM, Tristan Croll <<a href="mailto:tic20@cam.ac.uk" class="">tic20@cam.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="content-type" content="text/html; charset=utf-8" class=""><div dir="auto" class="">Currently, I think the shell is your friend here. First, select the two sulfurs. Then, in the shell:<div class=""><br class=""></div><div class="">from chimerax.atomic import selected_atoms</div><div class="">sel=selected_atoms(session)</div><div class="">m = sel.unique_structures[0]</div><div class="">m.new_bond(*sel)<br class=""><br class=""><div dir="ltr" class=""><div class="">- Tristan</div><div class=""> </div><div class=""><br class=""></div><div class=""> </div></div><div dir="ltr" class=""><br class="">On 7 Apr 2020, at 12:24, Mutum YAikhombA <<a href="mailto:mutum.yaikhomba@mrc-mbu.cam.ac.uk" class="">mutum.yaikhomba@mrc-mbu.cam.ac.uk</a>> wrote:<br class=""><br class=""></div><blockquote type="cite" class=""><div dir="ltr" class=""><meta http-equiv="Content-Type" content="text/html; charset=utf-8" class=""><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi </div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><br class=""><div class="">I was trying to make new disulphide bonds between a pair of cysteine residues (say residue numbers 142 and 157) using ChimeraX. The standard Chimera command - 'bond' doesn’t work in ChimeraX.</div><div class="">I have gone through the structure editing tool and couldn’t find an equivalent tool. I found some command-line tools in this page (new-bond), but this seems to be not so straightforward to use - <a href="https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html#chimerax.atomic.structure.AtomicStructure" class="">https://www.rbvi.ucsf.edu/chimerax/docs/devel/bundles/atomic/src/atomic.html#chimerax.atomic.structure.AtomicStructure</a>.</div><div class=""><br class=""></div><div class="">Could you please help?</div><div class="">Thanks</div><div class="">Yaikhomba</div></div></div></blockquote><blockquote type="cite" class=""><div dir="ltr" class=""><span class="">_______________________________________________</span><br class=""><span class="">ChimeraX-users mailing list</span><br class=""><span class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a></span><br class=""><span class="">Manage subscription:</span><br class=""><span class=""><a href="http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users" class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users</a></span><br class=""></div></blockquote></div></div>_______________________________________________<br class="">ChimeraX-users mailing list<br class=""><a href="mailto:ChimeraX-users@cgl.ucsf.edu" class="">ChimeraX-users@cgl.ucsf.edu</a><br class="">Manage subscription:<br class="">http://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users<br class=""></div></blockquote></div><br class=""></div></body></html>