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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. Can this script be modified to give the
minimum dimensions of the molecule (not just the x y z dimensions)? 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? This would be really nice to directly compare the
size of small molecules.<br><br>Many thanks <br><br><br><hr id="stopSpelling">CC: chimera-users@cgl.ucsf.edu<br>From: pett@cgl.ucsf.edu<br>To: le_monk@hotmail.com<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. <a href='http://clk.atdmt.com/UKM/go/197222280/direct/01/' target='_new'>Sign-up now.</a></body>
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