<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">The Python to place a helium atom named He1 at position <i class="">x</i><span style="font-style: normal;" class="">,</span><i class="">y</i><span style="font-style: normal;" class="">,</span><i class="">z</i><span style="font-style: normal;" class=""> is:</span><div class=""><br class=""></div><div class="">from BuildStructure import placeHelium</div><div class="">from chimera import Point</div><div class="">atom = placeHelium(<i class="">residue_name</i><span style="font-style: normal;" class="">, position=Point(</span><i class="">x,y,z</i><span style="font-style: normal;" class="">))</span></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 Dec 15, 2020, at 8:16 AM, Elaine Meng <<a href="mailto:meng@cgl.ucsf.EDU" class="">meng@cgl.ucsf.EDU</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Hi Yasser,<br class="">Chimera does not have a command to do this.  In Chimera you could do it with menu Tools... Structure Editing... Build Structure, the "Start Structure" atom option.  I don't know python, so I can't give details on that.<br class=""><<a href="https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start" class="">https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/editing.html#start</a>"><br class=""><br class="">Other possibilities in Chimera are to manually create (with a text editor) a PDB file or marker file and then open it.<br class=""><br class="">If you use ChimeraX instead, there is a "build start atom" command to do it.<br class=""><<a href="https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start" class="">https://rbvi.ucsf.edu/chimerax/docs/user/commands/build.html#start</a>><br class=""><br class="">I hope this helps,<br class="">Elaine<br class="">-----<br class="">Elaine C. Meng, Ph.D.                       <br class="">UCSF Chimera(X) team<br class="">Department of Pharmaceutical Chemistry<br class="">University of California, San Francisco<br class=""><br class=""><br class=""><blockquote type="cite" class="">On Dec 15, 2020, at 2:02 AM, Yasser Almeida <<a href="mailto:yasser.almeida@gmail.com" class="">yasser.almeida@gmail.com</a>> wrote:<br class=""><br class="">Hello,<br class=""><br class="">How can I create an atom object, with a given xyz coordinates, via command or python? <br class=""><br class="">Thanks in advance,<br class=""><br class="">Yasser<br class=""></blockquote><br class=""><br class="">_______________________________________________<br class="">Chimera-users mailing list: <a href="mailto:Chimera-users@cgl.ucsf.edu" class="">Chimera-users@cgl.ucsf.edu</a><br class="">Manage subscription: <a href="https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" class="">https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br class=""></div></div></blockquote></div><br class=""></div></body></html>