In order to inspect the 3D structure of CGCGTTTTCGCG and to
assign the 'stepping stones' you will need to practice
measuring interatomic distances using the SYBYL program. Log
into a Silicon Graphics terminal in room 336B and run the SYBYL
program by typing sybyl from a Unix command line prompt.
When a prompt is reached within the sybyl program, type noesy;
A "floating" menu will appear on the screen;
Click with the left mouse button on NOESY, then on
dna or CI2 in the next menu.
The picture on the screen can be translated by pressing the
middle mouse button, or rotated by pressing the right mouse
button. To resize the molecule, press both middle and right
buttons and move the mouse up (to enlarge) or down (to
decrease). Note that all these conventions are quite different
from the MacroModel program! To measure a distance between two
atoms, select distance with the left mouse button, then
ADD, then click on pairs of atoms with the left mouse
button. To display the distance, click on End Select. By
carefuly inspecting for close (<4.5Å) inter-proton
contacts, a detailed analysis of the nOe map can be
accomplished.
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