[Chimera-users] Trouble understanding intersurf results

[Kenward Vaughan]

Hello,

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.

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.

The command I use is

intersurf   :.b   :.k,.m   pair atom   prune 3 bias 0.5   select true

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.

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?

This is a fresh surface, BTW, and not created after something done prior 
to these steps.

Chimera version 1.14

Many thanks for your thoughts, and hope people are staying safe!


Kenward

-- 
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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