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
