Dear Jmol users,
I was trying to compare several molecular visualizers for viewing =
scorpion alfa toxins. Accordingly to the PDB files of the crystallized =
proteins, these toxins have de motif alfa-beta-beta-beta, but when using =
several molecular visualizers, including Jmol there are several =
different patterns. What does it mean?.
I should suppose that the molecule has the motif previously stated, but, =
surprisingly, when I used a combination of several mollecular =
visualizers, I could establish different groups of toxins (theoretically =
all of them should have the same motif), and these groups have =
functional significance, so.... I don't understand, have I found an =
emergent feature of these structures or I'm completely wrong?
Thanks for helping
Centro de Investigaciones en Ciencias de la Salud
Escuela de Ciencias de la Salud
Universidad de Oriente, N=FAcleo de Anzo=E1tegui
I'm only guessing, but the differences you see may be due to
different algorithms used for evaluating the secondary structure
motifs in different viewer programs.
For example, a beta strand takes different lengths on "cartoon"
rendering depending on the program used.
But anyway your observation sounds very interesting. Maybe some
proteins have a more strict pattern than others, and so you identifiy