<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><span class="Apple-tab-span" style="white-space:pre"> </span>Well, it certainly could be done by a custom Python script, e.g.:<div class=""><br class=""></div><div class="">from chimera import openModels, Molecule, selection</div><div class="">sel_atoms = []</div><div class="">for m in openModels.list(modelTypes=[Molecule]):</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>for a in m.atoms:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>x, y, z = a.coord().data()</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>if x0 <= x <= x1 and y0 <= y <= y1 and z0 <= z <= z1:</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>sel_atoms.append(a)</div><div class="">selection.setCurrent(sel_atoms)</div><div class=""><br class=""></div><div class="">This selection is working on the original coordinates, i.e. as provided by the input source. If you want to include rotations/translations that occurred in Chimera, you would use the .xformCoord() method instead of the .coord() method.</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>But perhaps if you described <i class="">why</i> you need to select atoms within a certain Cartesian box, we could provide better help.</div><div class=""><br class=""></div><div class="">—Eric</div><div class=""><br class=""><div class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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=""></div><div><blockquote type="cite" class=""><div class="">On Oct 31, 2016, at 11:37 AM, Cherry Dons <<a href="mailto:cherrydons@gmail.com" class="">cherrydons@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hi Chimera Developers,<div class=""><br class=""></div><div class="">This is Dengpan, one of chimera users. I have a question about how to select atoms within a region? For example, I I want to select atoms within a rectangular region </div><div class="">x0 to x1,</div><div class="">y0 to y1,</div><div class="">z0 to z1.</div><div class=""><br class=""></div><div class="">Could you please give me a hint how to do it? Thanks.</div><div class=""><br class=""></div><div class="">Dengpan Dong</div><div class=""><div class=""><br class=""></div>-- <div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr" class=""><div class="">Department of Materials Science and Engineering,</div><div class="">University of Utah</div></div></div>
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