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Another idea is use the "measure inertia" command<br>
<br>
<a class="moz-txt-link-freetext" href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#inertia</a><br>
<br>
which prints the principal axes of inertia of the molecule and their
lengths in the Reply Log.<br>
<br>
Tom<br>
<br>
<br>
-------- Original Message --------<br>
Subject: Re: [Chimera-users] Small molecule dimensions<br>
From: Eric Pettersen <a class="moz-txt-link-rfc2396E" href="mailto:pett@cgl.ucsf.edu"><pett@cgl.ucsf.edu></a><br>
To: le monk <a class="moz-txt-link-rfc2396E" href="mailto:le_monk@hotmail.com"><le_monk@hotmail.com></a><br>
Date: 4/21/10 11:37 AM<br>
<blockquote cite="mid:B4E71D2F-1BBD-4363-BB7A-FFEF91B71370@cgl.ucsf.edu"
type="cite">
<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-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 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-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 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-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 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 moz-do-not-send="true"
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
moz-do-not-send="true" href="mailto:chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a><br>
From:<span class="Apple-converted-space"> </span><a
moz-do-not-send="true" href="mailto:pett@cgl.ucsf.edu">pett@cgl.ucsf.edu</a><br>
To:<span class="Apple-converted-space"> </span><a moz-do-not-send="true"
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
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</span></blockquote>
</div>
<br>
</div>
<br>
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</blockquote>
</div>
<br>
<pre wrap="">
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</blockquote>
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