Thanks Bob for the extensive explanation of the parameters. It's very exciting
to find that the tool you designed can predict the very same results as the
ones from books/articles.
I have a question regarding one of the interactions figured in the last example
(106%) : a second contact ties Val6:B to Asp73, involving Carbon Gamma. But
this last contact "goes through" an oxygen atom from the carboxylate which
sounds strange to me ? Am I missing something there ?
-Paul
Le 23 juin 2011 à 18:39, Robert Hanson a écrit :
> Paul -- the parameters that are helpful here include the van der Waals radius
> to use and the second (target) atom set:
>
> contact ID "contact1" hydrophobic {val6:H} {!:H} 100%
>
> My analysis is here: http://stolaf.edu/people/hansonr/jmol/contact/2hbs.htm
>
> Looks like 100% gives you the strongest two Ala70 and Asp73,
> then changing that a bit more gives you:
>
> 101% Phe85
> 104% Leu88
> 106% Thr84
>
> I think the fact that we can even discuss this so succinctly proves my point
> that the CONTACT command with the CONNECT option could be useful.
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