<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>On Apr 21, 2010, at 11:20 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; ">Thank you Eric - this is really helpful. But as these are minimum x y z lengths then the reported dimensions will be different if the molecules coordinates were transformed.</div></span></blockquote><div><br></div>The function used in the script (coord()) uses untransformed coordinates. xformcoord() would use transformed coordinates.</div><div><br><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; ">Can this script be modified to give the minimum dimensions of the molecule (not just the x y z dimensions)?</div></span></blockquote><div><br></div>What would be the algorithm for computing that?</div><div><br><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; ">For example, can a box be drawn around the Van der Waal radii whose volume was the minimum possible for that molecule, and report the lengths of each of its dimensions?</div></span></blockquote><div><br></div>Again, how?</div><div><br></div><div>You can get a rough estimate by using the Axes tool to draw an axis along the principal axis of the molecule, with the axis radius equal to the average atom-atom distance from the axis. The axes information can be saved to a file.</div><div><br></div><div><a href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes">http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes</a></div><div><br></div><div>--Eric</div><div><br><blockquote type="cite"><div class="hmmessage" style="font-size: 10pt; font-family: Verdana; ">This would be really nice to directly compare the size of small molecules.<br><br>Many thanks<span class="Apple-converted-space"> </span><br><br><br><hr id="stopSpelling">CC:<span class="Apple-converted-space"> </span><a href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>From:<span class="Apple-converted-space"> </span><a href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a><br>To:<span class="Apple-converted-space"> </span><a href="mailto:le_monk@hotmail.com">le_monk@hotmail.com</a><br>Subject: Re: [Chimera-users] Small molecule dimensions<br>Date: Sun, 18 Apr 2010 07:52:31 -0700<br><br>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="ecxApple-tab-span" style="white-space: pre; "> </span>print m.name</div><div><span class="ecxApple-tab-span" style="white-space: pre; "> </span>atoms = m.atoms</div><div><span class="ecxApple-tab-span" style="white-space: pre; "> </span>for dim in range(3):</div><div><span class="ecxApple-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="ecxApple-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="ecxApple-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="ecxApple-tab-span" style="white-space: pre; "> </span>Eric Pettersen</div><div><span class="ecxApple-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="ecxApple-interchange-newline"><blockquote><span class="ecxApple-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; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; "><div class="ecxhmmessage" 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="ecxApple-converted-space"> </span><a href="http://clk.atdmt.com/UKM/go/197222280/direct/01/">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><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></div></blockquote></div><br></body></html>