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<p><font size="+1">Hello,</font></p>
<p><font size="+1">I'm trying to prepare a project tutorial for my
students; they are charged with illustrating the interactions
between the Fab portion of an antibody and its epitope
(antigen?--being a chemist having taken biology in 10th
grade...). In working to learn how to do this I've come across
a perplexing result using intersurf. <br>
</font></p>
<p><font size="+1">My working model is 1afv. After muddling around
with the graphical Intersurf panel trying to "fuse" two surface
results together, I realized that I could do it using the
command line. In the model I chose to highlight the interface
between chain B and both the K and M chains. I had already
learned how to apply the histogram threshold limits to the
command line results for coloration. <br>
</font></p>
<p><font size="+1">The command I use is</font></p>
<p><font size="+1">intersurf :.b :.k,.m pair atom prune 3
bias 0.5 select true</font></p>
<p><font size="+1">followed by adjusting the transparency. The
result surprised me, both before and after lighting up the atoms
and bonds. I've attached a (hopefully small) jpg. <br>
</font></p>
<p><font size="+1">My questions are (1) if the pruning distance is 3
(just playing around with distances) why is the surface shown so
obviously over-sized for such a small distance, and (2) why are
there residues selected which are (again) so far away from the
interface? <br>
</font></p>
<p><font size="+1">This is a fresh surface, BTW, and not created
after something done prior to these steps.</font></p>
<p><font size="+1">Chimera version 1.14</font></p>
<p><font size="+1">Many thanks for your thoughts, and hope people
are staying safe!</font></p>
<p><font size="+1"><br>
</font></p>
<p><font size="+1">Kenward</font><br>
</p>
<pre class="moz-signature" cols="72">--
In a completely rational society, the best of us would aspire to be
_teachers_ and the rest of us would have to settle for something less,
because passing civilization along from one generation to the next
ought to be the highest honor and the highest responsibility anyone
could have. - Lee Iacocca
Any fool can know. The point is to understand. - Albert Einstein
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