<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Yes, something like this:<div><br></div><div>from chimera import openModels, Molecule</div><div>for m in openModels.list(modelTypes=[Molecule]):</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>print m.name</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>atoms = m.atoms</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>for dim in range(3):</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>atoms.sort(lambda a1, a2, dim=dim: cmp(a1.coord().data()[dim], a2.coord().data()[dim]))</div><div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>print "minimum %s: %g" % ("xyz"[dim], atoms[0].coord().data()[dim] - atoms[0].radius)</div><div><div><span class="Apple-tab-span" style="white-space: pre; "> </span>print "maximum %s: %g" % ("xyz"[dim], atoms[-1].coord().data()[dim] - atoms[-1].radius)</div><div><br></div><div>Put the above in a file ending in ".py" and open it in Chimera and it will print the min/max xyz values accounting for radius in the Reply Log.</div><div><br></div><div>--Eric</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Eric Pettersen</div><div><span class="Apple-tab-span" style="white-space:pre"> </span>UCSF Computer Graphics Lab</div><div><br></div></div></div><div><div><div>On Apr 16, 2010, at 10:46 AM, le monk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">Hello,<br><br>I have a few pdb files of small molecules that I would like to know the dimensions of. Is it possible to use Chimera the measure the minimum x y z lengths - taking into account Van der Waals radii? Or perhaps you could suggest other software for this?<br><br>Many thanks<br><br><hr>Get a free e-mail account with Hotmail.<span class="Apple-converted-space"> </span><a href="http://clk.atdmt.com/UKM/go/197222280/direct/01/" target="_new">Sign-up now.</a>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br><a href="http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users">http://www.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></span></blockquote></div><br></div></body></html>