Re: AMBER: questions regarding JTREE

From: Bill Ross <>
Date: Wed, 27 Oct 2004 10:53:39 -0700 (PDT)

> I guess the JTREE is what I should go for, but the manual isn't very
> helpful at this point...
> What does M, S, B, 3, E mean for a) proteins, b) DNA?

The JTREE values are assigned by leap on a purely topological
basis and are somewhat arbitrary. For any residue with a connect0
and a connect1 atom, the shortest 'main chain' is found between
those atoms (if there is more than one path of minimal length,
one is selected arbitrarily). These are labeled JTREE=M. The
other atoms are labeled S, B, 3, and E according to their topological
positions and the order they are 'seen' by the algorithm. The
descriptions of the types was in the 'prep' doc which used to be
on the amber web and may still be there. Approximately from memory:

  S - side chain?
  B - branch (atom w/ 3 bonds)
  3 - 3-way branch (4 bonds)
  E - end (1 bond)

Ring-closing bonds (arbitrarily selected) are not counted in the tree
type definitions, and are specified in the LOOP section of the

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Oct 27 2004 - 19:53:00 PDT
Custom Search