<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=""><br class=""></div><div class=""> One more hacky way to add a bond, the "marker link" command. The marker command is intended to place markers on density maps and link them to trace paths. But it really just makes atoms and bonds. So to make your disulphide bond between residues 3 and 16:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>marker link :3,16@SG radius 0.2</div><div class=""><br class=""></div><div class="">This makes bond color yellow instead of matching the atoms, to remedy that:</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>color :3,16@SG halfbond true</div><div class=""><br class=""></div><div class="">You could make an alias to do these two commands</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>alias bond marker link $1 radius 0.2 ; color $1 halfbond true</div><div class=""><br class=""></div><div class="">then just use</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>bond :3,16@SG</div><div class=""><br class=""></div><div class=""> Tom</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On Apr 7, 2020, at 4:24 AM, Mutum YAikhombA <<a href="mailto:mutum.yaikhomba@mrc-mbu.cam.ac.uk" class="">mutum.yaikhomba@mrc-mbu.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 style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" 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>_______________________________________________<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>